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\begin{document} |
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\preprint{AIP/123-QED} |
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%\preprint{AIP/123-QED} |
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\title[Efficient electrostatics for condensed-phase multipoles]{Real space alternatives to the Ewald |
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Sum. II. Comparison of Simulation Methodologies} % Force line breaks with \\ |
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\title{Real space electrostatics for multipoles. II. Comparisons with |
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the Ewald Sum} |
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\author{Madan Lamichhane} |
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\affiliation{Department of Physics, University |
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of Notre Dame, Notre Dame, IN 46556}%Lines break automatically or can be forced with \\ |
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\affiliation{Department of Physics, University of Notre Dame, Notre Dame, IN 46556} |
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\author{Kathie E. Newman} |
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\affiliation{Department of Physics, University |
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of Notre Dame, Notre Dame, IN 46556} |
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\affiliation{Department of Physics, University of Notre Dame, Notre Dame, IN 46556} |
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\author{J. Daniel Gezelter}% |
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\email{gezelter@nd.edu.} |
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\affiliation{Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556%\\This line break forced with \textbackslash\textbackslash |
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}% |
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\affiliation{Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 |
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} |
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\date{\today}% It is always \today, today, |
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% but any date may be explicitly specified |
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\date{\today} |
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\begin{abstract} |
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We have tested our recently developed shifted potential, gradient-shifted force, and Taylor-shifted force methods for the higher-order multipoles against Ewald’s method in different types of liquid and crystalline system. In this paper, we have also investigated the conservation of total energy in the molecular dynamic simulation using all of these methods. The shifted potential method shows better agreement with the Ewald in the energy differences between different configurations as compared to the direct truncation. Both the gradient shifted force and Taylor-shifted force methods reproduce very good energy conservation. But the absolute energy, force and torque evaluated from the gradient shifted force method shows better result as compared to taylor-shifted force method. Hence the gradient-shifted force method suitably mimics the electrostatic interaction in the molecular dynamic simulation. |
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We report on tests of the shifted potential (SP), gradient shifted |
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force (GSF), and Taylor shifted force (TSF) real-space methods for |
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multipole interactions developed in the first paper in this series, |
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using the multipolar Ewald sum as a reference method. The tests were |
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carried out in a variety of condensed-phase environments designed to |
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test up to quadrupole-quadrupole interactions. Comparisons of the |
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energy differences between configurations, molecular forces, and |
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torques were used to analyze how well the real-space models perform |
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relative to the more computationally expensive Ewald treatment. We |
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have also investigated the energy conservation, structural, and |
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dynamical properties of the new methods in molecular dynamics |
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simulations. The SP method shows excellent agreement with |
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configurational energy differences, forces, and torques, and would |
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be suitable for use in Monte Carlo calculations. Of the two new |
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shifted-force methods, the GSF approach shows the best agreement |
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with Ewald-derived energies, forces, and torques and also exhibits |
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energy conservation properties that make it an excellent choice for |
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efficient computation of electrostatic interactions in molecular |
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dynamics simulations. Both SP and GSF are able to reproduce |
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structural and dynamical properties in the liquid models with |
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excellent fidelity. |
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\end{abstract} |
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|
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\pacs{Valid PACS appear here}% PACS, the Physics and Astronomy |
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%\pacs{Valid PACS appear here}% PACS, the Physics and Astronomy |
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% Classification Scheme. |
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\keywords{Electrostatics, Multipoles, Real-space} |
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%\keywords{Electrostatics, Multipoles, Real-space} |
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\maketitle |
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|
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– |
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\section{\label{sec:intro}Introduction} |
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Computing the interactions between electrostatic sites is one of the |
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most expensive aspects of molecular simulations, which is why there |
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have been significant efforts to develop practical, efficient and |
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< |
convergent methods for handling these interactions. Ewald's method is |
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perhaps the best known and most accurate method for evaluating |
| 102 |
< |
energies, forces, and torques in explicitly-periodic simulation |
| 103 |
< |
cells. In this approach, the conditionally convergent electrostatic |
| 104 |
< |
energy is converted into two absolutely convergent contributions, one |
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which is carried out in real space with a cutoff radius, and one in |
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reciprocal space.\cite{Clarke:1986eu,Woodcock75} |
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most expensive aspects of molecular simulations. There have been |
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significant efforts to develop practical, efficient and convergent |
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> |
methods for handling these interactions. Ewald's method is perhaps the |
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best known and most accurate method for evaluating energies, forces, |
| 102 |
> |
and torques in explicitly-periodic simulation cells. In this approach, |
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the conditionally convergent electrostatic energy is converted into |
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two absolutely convergent contributions, one which is carried out in |
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real space with a cutoff radius, and one in reciprocal |
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space.\cite{Ewald21,deLeeuw80,Smith81,Allen87} |
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|
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When carried out as originally formulated, the reciprocal-space |
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portion of the Ewald sum exhibits relatively poor computational |
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scaling, making it prohibitive for large systems. By utilizing |
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particle meshes and three dimensional fast Fourier transforms (FFT), |
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the particle-mesh Ewald (PME), particle-particle particle-mesh Ewald |
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(P\textsuperscript{3}ME), and smooth particle mesh Ewald (SPME) methods can decrease |
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the computational cost from $O(N^2)$ down to $O(N \log |
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N)$.\cite{Takada93,Gunsteren94,Gunsteren95,Darden:1993pd,Essmann:1995pb}. |
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scaling, making it prohibitive for large systems. By utilizing a |
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particle mesh and three dimensional fast Fourier transforms (FFT), the |
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particle-mesh Ewald (PME), particle-particle particle-mesh Ewald |
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(P\textsuperscript{3}ME), and smooth particle mesh Ewald (SPME) |
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methods can decrease the computational cost from $O(N^2)$ down to $O(N |
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\log |
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N)$.\cite{Takada93,Gunsteren94,Gunsteren95,Darden:1993pd,Essmann:1995pb} |
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|
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Because of the artificial periodicity required for the Ewald sum, the |
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method may require modification to compute interactions for |
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Because of the artificial periodicity required for the Ewald sum, |
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interfacial molecular systems such as membranes and liquid-vapor |
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interfaces.\cite{Parry:1975if,Parry:1976fq,Clarke77,Perram79,Rhee:1989kl} |
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To simulate interfacial systems, Parry’s extension of the 3D Ewald sum |
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is appropriate for slab geometries.\cite{Parry:1975if} The inherent |
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periodicity in the Ewald’s method can also be problematic for |
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interfacial molecular systems.\cite{Fennell:2006lq} Modified Ewald |
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methods that were developed to handle two-dimensional (2D) |
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electrostatic interactions in interfacial systems have not had similar |
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particle-mesh treatments.\cite{Parry:1975if, Parry:1976fq, Clarke77, |
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Perram79,Rhee:1989kl,Spohr:1997sf,Yeh:1999oq} |
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interfaces require modifications to the method. Parry's extension of |
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the three dimensional Ewald sum is appropriate for slab |
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geometries.\cite{Parry:1975if} Modified Ewald methods that were |
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developed to handle two-dimensional (2-D) electrostatic |
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interactions.\cite{Parry:1975if,Parry:1976fq,Clarke77,Perram79,Rhee:1989kl} |
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These methods were originally quite computationally |
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expensive.\cite{Spohr97,Yeh99} There have been several successful |
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efforts that reduced the computational cost of 2-D lattice summations, |
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bringing them more in line with the scaling for the full 3-D |
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treatments.\cite{Yeh99,Kawata01,Arnold02,deJoannis02,Brodka04} The |
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inherent periodicity required by the Ewald method can also be |
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problematic in a number of protein/solvent and ionic solution |
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environments.\cite{Roberts94,Roberts95,Luty96,Hunenberger99a,Hunenberger99b,Weber00,Fennell:2006lq} |
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|
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\subsection{Real-space methods} |
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Wolf \textit{et al.}\cite{Wolf:1999dn} proposed a real space $O(N)$ |
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method for calculating electrostatic interactions between point |
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charges. They argued that the effective Coulomb interaction in |
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condensed systems is actually short ranged.\cite{Wolf92,Wolf95}. For |
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an ordered lattice (e.g. when computing the Madelung constant of an |
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ionic solid), the material can be considered as a set of ions |
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interacting with neutral dipolar or quadrupolar ``molecules'' giving |
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an effective distance dependence for the electrostatic interactions of |
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$r^{-5}$ (see figure \ref{fig:NaCl}. For this reason, careful |
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applications of Wolf's method are able to obtain accurate estimates of |
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Madelung constants using relatively short cutoff radii. Recently, |
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Fukuda used neutralization of the higher order moments for the |
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calculation of the electrostatic interaction of the point charges |
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system.\cite{Fukuda:2013sf} |
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charges. They argued that the effective Coulomb interaction in most |
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condensed phase systems is effectively short |
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ranged.\cite{Wolf92,Wolf95} For an ordered lattice (e.g., when |
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computing the Madelung constant of an ionic solid), the material can |
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be considered as a set of ions interacting with neutral dipolar or |
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quadrupolar ``molecules'' giving an effective distance dependence for |
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the electrostatic interactions of $r^{-5}$ (see figure |
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\ref{fig:schematic}). If one views the \ce{NaCl} crystal as a simple |
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cubic (SC) structure with an octupolar \ce{(NaCl)4} basis, the |
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electrostatic energy per ion converges more rapidly to the Madelung |
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energy than the dipolar approximation.\cite{Wolf92} To find the |
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correct Madelung constant, Lacman suggested that the NaCl structure |
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could be constructed in a way that the finite crystal terminates with |
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complete \ce{(NaCl)4} molecules.\cite{Lacman65} The central ion sees |
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what is effectively a set of octupoles at large distances. These facts |
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suggest that the Madelung constants are relatively short ranged for |
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perfect ionic crystals.\cite{Wolf:1999dn} For this reason, careful |
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application of Wolf's method can provide accurate estimates of |
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Madelung constants using relatively short cutoff radii. |
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|
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\begin{figure}[h!] |
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Direct truncation of interactions at a cutoff radius creates numerical |
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errors. Wolf \textit{et al.} suggest that truncation errors are due |
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to net charge remaining inside the cutoff sphere.\cite{Wolf:1999dn} To |
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neutralize this charge they proposed placing an image charge on the |
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surface of the cutoff sphere for every real charge inside the cutoff. |
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> |
These charges are present for the evaluation of both the pair |
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interaction energy and the force, although the force expression |
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maintains a discontinuity at the cutoff sphere. In the original Wolf |
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formulation, the total energy for the charge and image were not equal |
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to the integral of the force expression, and as a result, the total |
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energy would not be conserved in molecular dynamics (MD) |
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simulations.\cite{Zahn:2002hc} Zahn \textit{et al.}, and Fennell and |
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Gezelter later proposed shifted force variants of the Wolf method with |
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commensurate force and energy expressions that do not exhibit this |
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problem.\cite{Zahn:2002hc,Fennell:2006lq} Related real-space methods |
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were also proposed by Chen \textit{et |
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al.}\cite{Chen:2004du,Chen:2006ii,Denesyuk:2008ez,Rodgers:2006nw} |
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and by Wu and Brooks.\cite{Wu:044107} Recently, Fukuda has successfully |
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used additional neutralization of higher order moments for systems of |
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point charges.\cite{Fukuda:2013sf} |
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|
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\begin{figure} |
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\centering |
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\includegraphics[width=0.50 \textwidth]{chargesystem.pdf} |
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\caption{Top: NaCl crystal showing how spherical truncation can |
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breaking effective charge ordering, and how complete \ce{(NaCl)4} |
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molecules interact with the central ion. Bottom: A dipolar |
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crystal exhibiting similar behavior and illustrating how the |
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effective dipole-octupole interactions can be disrupted by |
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spherical truncation.} |
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\label{fig:NaCl} |
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\includegraphics[width=\linewidth]{schematic.eps} |
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\caption{Top: Ionic systems exhibit local clustering of dissimilar |
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charges (in the smaller grey circle), so interactions are |
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effectively charge-multipole at longer distances. With hard |
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cutoffs, motion of individual charges in and out of the cutoff |
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sphere can break the effective multipolar ordering. Bottom: |
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dipolar crystals and fluids have a similar effective |
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\textit{quadrupolar} ordering (in the smaller grey circles), and |
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orientational averaging helps to reduce the effective range of the |
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interactions in the fluid. Placement of reversed image multipoles |
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on the surface of the cutoff sphere recovers the effective |
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higher-order multipole behavior. \label{fig:schematic}} |
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\end{figure} |
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|
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The direct truncation of interactions at a cutoff radius creates |
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truncation defects. Wolf \textit{et al.} further argued that |
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truncation errors are due to net charge remaining inside the cutoff |
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sphere.\cite{Wolf:1999dn} To neutralize this charge they proposed |
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placing an image charge on the surface of the cutoff sphere for every |
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real charge inside the cutoff. These charges are present for the |
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evaluation of both the pair interaction energy and the force, although |
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the force expression maintained a discontinuity at the cutoff sphere. |
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< |
In the original Wolf formulation, the total energy for the charge and |
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image were not equal to the integral of their force expression, and as |
| 150 |
< |
a result, the total energy would not be conserved in molecular |
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< |
dynamics (MD) simulations.\cite{Zahn:2002hc} Zahn \textit{et al.} and |
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Fennel and Gezelter later proposed shifted force variants of the Wolf |
| 153 |
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method with commensurate force and energy expressions that do not |
| 154 |
< |
exhibit this problem.\cite{Fennell:2006lq} Related real-space |
| 155 |
< |
methods were also proposed by Chen \textit{et |
| 156 |
< |
al.}\cite{Chen:2004du,Chen:2006ii,Denesyuk:2008ez,Rodgers:2006nw} |
| 157 |
< |
and by Wu and Brooks.\cite{Wu:044107} |
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< |
|
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< |
Considering the interaction of one central ion in an ionic crystal |
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< |
with a portion of the crystal at some distance, the effective Columbic |
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potential is found to be decreasing as $r^{-5}$. If one views the |
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\ce{NaCl} crystal as simple cubic (SC) structure with an octupolar |
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\ce{(NaCl)4} basis, the electrostatic energy per ion converges more |
| 164 |
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rapidly to the Madelung energy than the dipolar |
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< |
approximation.\cite{Wolf92} To find the correct Madelung constant, |
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Lacman suggested that the NaCl structure could be constructed in a way |
| 167 |
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that the finite crystal terminates with complete \ce{(NaCl)4} |
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molecules.\cite{Lacman65} Any charge in a NaCl crystal is surrounded |
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< |
by opposite charges. Similarly for each pair of charges, there is an |
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opposite pair of charge adjacent to it. The central ion sees what is |
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< |
effectively a set of octupoles at large distances. These facts suggest |
| 172 |
< |
that the Madelung constants are relatively short ranged for perfect |
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< |
ionic crystals.\cite{Wolf:1999dn} |
| 174 |
< |
|
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One can make a similar argument for crystals of point multipoles. The |
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Luttinger and Tisza treatment of energy constants for dipolar lattices |
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< |
utilizes 24 basis vectors that contain dipoles at the eight corners of |
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a unit cube. Only three of these basis vectors, $X_1, Y_1, |
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\mathrm{~and~} Z_1,$ retain net dipole moments, while the rest have |
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zero net dipole and retain contributions only from higher order |
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< |
multipoles. The effective interaction between a dipole at the center |
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One can make a similar effective range argument for crystals of point |
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> |
\textit{multipoles}. The Luttinger and Tisza treatment of energy |
| 196 |
> |
constants for dipolar lattices utilizes 24 basis vectors that contain |
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> |
dipoles at the eight corners of a unit cube.\cite{LT} Only three of |
| 198 |
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these basis vectors, $X_1, Y_1, \mathrm{~and~} Z_1,$ retain net dipole |
| 199 |
> |
moments, while the rest have zero net dipole and retain contributions |
| 200 |
> |
only from higher order multipoles. The lowest-energy crystalline |
| 201 |
> |
structures are built out of basis vectors that have only residual |
| 202 |
> |
quadrupolar moments (e.g. the $Z_5$ array). In these low energy |
| 203 |
> |
structures, the effective interaction between a dipole at the center |
| 204 |
|
of a crystal and a group of eight dipoles farther away is |
| 205 |
|
significantly shorter ranged than the $r^{-3}$ that one would expect |
| 206 |
|
for raw dipole-dipole interactions. Only in crystals which retain a |
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unstable. |
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|
|
| 212 |
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In ionic crystals, real-space truncation can break the effective |
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< |
multipolar arrangements (see Fig. \ref{fig:NaCl}), causing significant |
| 214 |
< |
swings in the electrostatic energy as the cutoff radius is increased |
| 215 |
< |
(or as individual ions move back and forth across the boundary). This |
| 216 |
< |
is why the image charges were necessary for the Wolf sum to exhibit |
| 217 |
< |
rapid convergence. Similarly, the real-space truncation of point |
| 218 |
< |
multipole interactions breaks higher order multipole arrangements, and |
| 219 |
< |
image multipoles are required for real-space treatments of |
| 198 |
< |
electrostatic energies. |
| 213 |
> |
multipolar arrangements (see Fig. \ref{fig:schematic}), causing |
| 214 |
> |
significant swings in the electrostatic energy as individual ions move |
| 215 |
> |
back and forth across the boundary. This is why the image charges are |
| 216 |
> |
necessary for the Wolf sum to exhibit rapid convergence. Similarly, |
| 217 |
> |
the real-space truncation of point multipole interactions breaks |
| 218 |
> |
higher order multipole arrangements, and image multipoles are required |
| 219 |
> |
for real-space treatments of electrostatic energies. |
| 220 |
|
|
| 221 |
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% Because of this reason, although the nature of electrostatic |
| 222 |
< |
% interaction short ranged, the hard cutoff sphere creates very large |
| 223 |
< |
% fluctuation in the electrostatic energy for the perfect crystal. In |
| 224 |
< |
% addition, the charge neutralized potential proposed by Wolf et |
| 225 |
< |
% al. converged to correct Madelung constant but still holds oscillation |
| 226 |
< |
% in the energy about correct Madelung energy.\cite{Wolf:1999dn}. This |
| 227 |
< |
% oscillation in the energy around its fully converged value can be due |
| 228 |
< |
% to the non-neutralized value of the higher order moments within the |
| 208 |
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% cutoff sphere. |
| 221 |
> |
The shorter effective range of electrostatic interactions is not |
| 222 |
> |
limited to perfect crystals, but can also apply in disordered fluids. |
| 223 |
> |
Even at elevated temperatures, there is local charge balance in an |
| 224 |
> |
ionic liquid, where each positive ion has surroundings dominated by |
| 225 |
> |
negative ions and vice versa. The reversed-charge images on the |
| 226 |
> |
cutoff sphere that are integral to the Wolf and damped shifted force |
| 227 |
> |
(DSF) approaches retain the effective multipolar interactions as the |
| 228 |
> |
charges traverse the cutoff boundary. |
| 229 |
|
|
| 230 |
< |
The forces and torques acting on atomic sites are the fundamental |
| 231 |
< |
factors driving dynamics in molecular simulations. Fennell and |
| 232 |
< |
Gezelter proposed the damped shifted force (DSF) energy kernel to |
| 233 |
< |
obtain consistent energies and forces on the atoms within the cutoff |
| 230 |
> |
In multipolar fluids (see Fig. \ref{fig:schematic}) there is |
| 231 |
> |
significant orientational averaging that additionally reduces the |
| 232 |
> |
effect of long-range multipolar interactions. The image multipoles |
| 233 |
> |
that are introduced in the Taylor shifted force (TSF), gradient |
| 234 |
> |
shifted force (GSF), and shifted potential (SP) methods mimic this effect |
| 235 |
> |
and reduce the effective range of the multipolar interactions as |
| 236 |
> |
interacting molecules traverse each other's cutoff boundaries. |
| 237 |
> |
|
| 238 |
> |
Forces and torques acting on atomic sites are fundamental in driving |
| 239 |
> |
dynamics in molecular simulations, and the DSF energy kernel provides |
| 240 |
> |
consistent energies and forces on charged atoms within the cutoff |
| 241 |
|
sphere. Both the energy and the force go smoothly to zero as an atom |
| 242 |
< |
aproaches the cutoff radius. The comparisons of the accuracy these |
| 242 |
> |
approaches the cutoff radius. The comparisons of the accuracy these |
| 243 |
|
quantities between the DSF kernel and SPME was surprisingly |
| 244 |
< |
good.\cite{Fennell:2006lq} The DSF method has seen increasing use for |
| 245 |
< |
calculating electrostatic interactions in molecular systems with |
| 246 |
< |
relatively uniform charge |
| 220 |
< |
densities.\cite{Shi:2013ij,Kannam:2012rr,Acevedo13,Space12,English08,Lawrence13,Vergne13} |
| 244 |
> |
good.\cite{Fennell:2006lq} As a result, the DSF method has seen |
| 245 |
> |
increasing use in molecular systems with relatively uniform charge |
| 246 |
> |
densities.\cite{English08,Kannam:2012rr,Space12,Lawrence13,Acevedo13,Shi:2013ij,Vergne13} |
| 247 |
|
|
| 248 |
|
\subsection{The damping function} |
| 249 |
< |
The damping function used in our research has been discussed in detail |
| 250 |
< |
in the first paper of this series.\cite{PaperI} The radial kernel |
| 251 |
< |
$1/r$ for the interactions between point charges can be replaced by |
| 252 |
< |
the complementary error function $\mathrm{erfc}(\alpha r)/r$ to |
| 253 |
< |
accelerate the rate of convergence, where $\alpha$ is a damping |
| 254 |
< |
parameter with units of inverse distance. Altering the value of |
| 255 |
< |
$\alpha$ is equivalent to changing the width of Gaussian charge |
| 256 |
< |
distributions that replace each point charge -- Gaussian overlap |
| 257 |
< |
integrals yield complementary error functions when truncated at a |
| 258 |
< |
finite distance. |
| 249 |
> |
The damping function has been discussed in detail in the first paper |
| 250 |
> |
of this series.\cite{PaperI} The $1/r$ Coulombic kernel for the |
| 251 |
> |
interactions between point charges can be replaced by the |
| 252 |
> |
complementary error function $\mathrm{erfc}(\alpha r)/r$ to accelerate |
| 253 |
> |
convergence, where $\alpha$ is a damping parameter with units of |
| 254 |
> |
inverse distance. Altering the value of $\alpha$ is equivalent to |
| 255 |
> |
changing the width of Gaussian charge distributions that replace each |
| 256 |
> |
point charge, as Coulomb integrals with Gaussian charge distributions |
| 257 |
> |
produce complementary error functions when truncated at a finite |
| 258 |
> |
distance. |
| 259 |
|
|
| 260 |
< |
By using suitable value of damping alpha ($\alpha \sim 0.2$) for a |
| 261 |
< |
cutoff radius ($r_{c}=9 A$), Fennel and Gezelter produced very good |
| 262 |
< |
agreement with SPME for the interaction energies, forces and torques |
| 263 |
< |
for charge-charge interactions.\cite{Fennell:2006lq} |
| 260 |
> |
With moderate damping coefficients, $\alpha \sim 0.2$ \AA$^{-1}$, the DSF method |
| 261 |
> |
produced very good agreement with SPME for interaction energies, |
| 262 |
> |
forces and torques for charge-charge |
| 263 |
> |
interactions.\cite{Fennell:2006lq} |
| 264 |
|
|
| 265 |
|
\subsection{Point multipoles in molecular modeling} |
| 266 |
|
Coarse-graining approaches which treat entire molecular subsystems as |
| 267 |
|
a single rigid body are now widely used. A common feature of many |
| 268 |
|
coarse-graining approaches is simplification of the electrostatic |
| 269 |
|
interactions between bodies so that fewer site-site interactions are |
| 270 |
< |
required to compute configurational energies. Many coarse-grained |
| 271 |
< |
molecular structures would normally consist of equal positive and |
| 246 |
< |
negative charges, and rather than use multiple site-site interactions, |
| 247 |
< |
the interaction between higher order multipoles can also be used to |
| 248 |
< |
evaluate a single molecule-molecule |
| 249 |
< |
interaction.\cite{Ren06,Essex10,Essex11} |
| 270 |
> |
required to compute configurational |
| 271 |
> |
energies.\cite{Ren06,Essex10,Essex11} |
| 272 |
|
|
| 273 |
< |
Because electrons in a molecule are not localized at specific points, |
| 274 |
< |
the assignment of partial charges to atomic centers is a relatively |
| 275 |
< |
rough approximation. Atomic sites can also be assigned point |
| 276 |
< |
multipoles and polarizabilities to increase the accuracy of the |
| 277 |
< |
molecular model. Recently, water has been modeled with point |
| 278 |
< |
multipoles up to octupolar |
| 279 |
< |
order.\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} Atom-centered point |
| 273 |
> |
Additionally, because electrons in a molecule are not localized at |
| 274 |
> |
specific points, the assignment of partial charges to atomic centers |
| 275 |
> |
is always an approximation. For increased accuracy, atomic sites can |
| 276 |
> |
also be assigned point multipoles and polarizabilities. Recently, |
| 277 |
> |
water has been modeled with point multipoles up to octupolar order |
| 278 |
> |
using the soft sticky dipole-quadrupole-octupole (SSDQO) |
| 279 |
> |
model.\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} Atom-centered point |
| 280 |
|
multipoles up to quadrupolar order have also been coupled with point |
| 281 |
|
polarizabilities in the high-quality AMOEBA and iAMOEBA water |
| 282 |
< |
models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk}. But |
| 283 |
< |
using point multipole with the real space truncation without |
| 284 |
< |
accounting for multipolar neutrality will create energy conservation |
| 285 |
< |
issues in molecular dynamics (MD) simulations. |
| 282 |
> |
models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk} However, |
| 283 |
> |
truncating point multipoles without smoothing the forces and torques |
| 284 |
> |
can create energy conservation issues in molecular dynamics |
| 285 |
> |
simulations. |
| 286 |
|
|
| 287 |
|
In this paper we test a set of real-space methods that were developed |
| 288 |
|
for point multipolar interactions. These methods extend the damped |
| 289 |
|
shifted force (DSF) and Wolf methods originally developed for |
| 290 |
|
charge-charge interactions and generalize them for higher order |
| 291 |
< |
multipoles. The detailed mathematical development of these methods has |
| 292 |
< |
been presented in the first paper in this series, while this work |
| 293 |
< |
covers the testing the energies, forces, torques, and energy |
| 291 |
> |
multipoles. The detailed mathematical development of these methods |
| 292 |
> |
has been presented in the first paper in this series, while this work |
| 293 |
> |
covers the testing of energies, forces, torques, and energy |
| 294 |
|
conservation properties of the methods in realistic simulation |
| 295 |
|
environments. In all cases, the methods are compared with the |
| 296 |
< |
reference method, a full multipolar Ewald treatment. |
| 296 |
> |
reference method, a full multipolar Ewald treatment.\cite{Smith82,Smith98} |
| 297 |
|
|
| 298 |
|
|
| 277 |
– |
%\subsection{Conservation of total energy } |
| 278 |
– |
%To conserve the total energy in MD simulations, the energy, force, and torque on a central molecule due to another molecule should smoothly tends to zero as second molecule approaches to cutoff radius. In addition, the force should be derivable from the energy and vice versa. If only the first condition holds but not the second, the total energy does not conserve.\cite{Fennell:2006lq}. The hard cutoff method does not ensure the smooth transition of the energy, force, and torque at the cutoff radius.\cite{Wolf:1999dn} By placing image charge on the surface of the cutoff sphere, the smooth transition of the energy can be ensured but the force and torque remains discontinuous. Therefore the purposed methods should have smooth transition of the energy, force and torque to ensure the total energy conservation and the expression should be close to idea of placing image multipole on the surface of the cutoff sphere. |
| 279 |
– |
|
| 299 |
|
\section{\label{sec:method}Review of Methods} |
| 300 |
|
Any real-space electrostatic method that is suitable for MD |
| 301 |
|
simulations should have the electrostatic energy, forces and torques |
| 302 |
|
between two sites go smoothly to zero as the distance between the |
| 303 |
< |
sites, $r_{\bf ab}$ approaches the cutoff radius, $r_c$. Requiring |
| 303 |
> |
sites, $r_{ab}$ approaches the cutoff radius, $r_c$. Requiring |
| 304 |
|
this continuity at the cutoff is essential for energy conservation in |
| 305 |
|
MD simulations. The mathematical details of the shifted potential |
| 306 |
|
(SP), gradient-shifted-force (GSF) and Taylor shifted-force (TSF) |
| 314 |
|
expressed as the product of two multipole operators and a Coulombic |
| 315 |
|
kernel, |
| 316 |
|
\begin{equation} |
| 317 |
< |
U_{\bf{ab}}(r)=\hat{M}_{\bf a} \hat{M}_{\bf b} \frac{1}{r} \label{kernel}. |
| 317 |
> |
U_{ab}(r)= M_{a} M_{b} \frac{1}{r} \label{kernel}. |
| 318 |
|
\end{equation} |
| 319 |
< |
where the multipole operator for site $\bf a$, |
| 320 |
< |
\begin{equation} |
| 321 |
< |
\hat{M}_{\bf a} = C_{\bf a} - D_{{\bf a}\alpha} \frac{\partial}{\partial r_{\alpha}} |
| 303 |
< |
+ Q_{{\bf a}\alpha\beta} |
| 304 |
< |
\frac{\partial^2}{\partial r_{\alpha} \partial r_{\beta}} + \dots |
| 305 |
< |
\end{equation} |
| 306 |
< |
is expressed in terms of the point charge, $C_{\bf a}$, dipole, |
| 307 |
< |
$D_{{\bf a}\alpha}$, and quadrupole, $Q_{{\bf a}\alpha\beta}$, for |
| 308 |
< |
object $\bf a$. Note that in this work, we use the primitive |
| 309 |
< |
quadrupole tensor, $Q_{a\alpha,\beta}=\frac{1}{2}\sum_{k\;in\;a}q_k |
| 310 |
< |
r_{k\alpha}r_{k\beta}$ to represent point quadrupoles on a site. |
| 319 |
> |
where the multipole operator for site $a$, $M_{a}$, is |
| 320 |
> |
expressed in terms of the point charge, $C_{a}$, dipole, ${\bf D}_{a}$, and quadrupole, $\mathsf{Q}_{a}$, for object |
| 321 |
> |
$a$, etc. |
| 322 |
|
|
| 323 |
< |
Interactions between multipoles can be expressed as higher derivatives |
| 324 |
< |
of the bare Coulomb potential, so one way of ensuring that the forces |
| 314 |
< |
and torques vanish at the cutoff distance is to include a larger |
| 315 |
< |
number of terms in the truncated Taylor expansion, e.g., |
| 316 |
< |
% |
| 323 |
> |
The TSF potential for any multipole-multipole interaction can be |
| 324 |
> |
written |
| 325 |
|
\begin{equation} |
| 318 |
– |
f_n^{\text{shift}}(r)=\sum_{m=0}^{n+1} \frac {(r-R_c)^m}{m!} f^{(m)} \Big \lvert _{R_c} . |
| 319 |
– |
\end{equation} |
| 320 |
– |
% |
| 321 |
– |
The combination of $f(r)$ with the shifted function is denoted $f_n(r)=f(r)-f_n^{\text{shift}}(r)$. |
| 322 |
– |
Thus, for $f(r)=1/r$, we find |
| 323 |
– |
% |
| 324 |
– |
\begin{equation} |
| 325 |
– |
f_1(r)=\frac{1}{r}- \frac{1}{R_c} + (r - R_c) \frac{1}{R_c^2} - \frac{(r-R_c)^2}{R_c^3} . |
| 326 |
– |
\end{equation} |
| 327 |
– |
This function is an approximate electrostatic potential that has |
| 328 |
– |
vanishing second derivatives at the cutoff radius, making it suitable |
| 329 |
– |
for shifting the forces and torques of charge-dipole interactions. |
| 330 |
– |
|
| 331 |
– |
In general, the TSF potential for any multipole-multipole interaction |
| 332 |
– |
can be written |
| 333 |
– |
\begin{equation} |
| 326 |
|
U^{\text{TSF}}= (\text{prefactor}) (\text{derivatives}) f_n(r) |
| 327 |
|
\label{generic} |
| 328 |
|
\end{equation} |
| 329 |
< |
with $n=0$ for charge-charge, $n=1$ for charge-dipole, $n=2$ for |
| 330 |
< |
charge-quadrupole and dipole-dipole, $n=3$ for dipole-quadrupole, and |
| 331 |
< |
$n=4$ for quadrupole-quadrupole. To ensure smooth convergence of the |
| 332 |
< |
energy, force, and torques, the required number of terms from Taylor |
| 333 |
< |
series expansion in $f_n(r)$ must be performed for different |
| 334 |
< |
multipole-multipole interactions. |
| 329 |
> |
where $f_n(r)$ is a shifted kernel that is appropriate for the order |
| 330 |
> |
of the interaction (see Ref. \onlinecite{PaperI}), with $n=0$ for |
| 331 |
> |
charge-charge, $n=1$ for charge-dipole, $n=2$ for charge-quadrupole |
| 332 |
> |
and dipole-dipole, $n=3$ for dipole-quadrupole, and $n=4$ for |
| 333 |
> |
quadrupole-quadrupole. To ensure smooth convergence of the energy, |
| 334 |
> |
force, and torques, a Taylor expansion with $n$ terms must be |
| 335 |
> |
performed at cutoff radius ($r_c$) to obtain $f_n(r)$. |
| 336 |
|
|
| 344 |
– |
To carry out the same procedure for a damped electrostatic kernel, we |
| 345 |
– |
replace $1/r$ in the Coulomb potential with $\text{erfc}(\alpha r)/r$. |
| 346 |
– |
Many of the derivatives of the damped kernel are well known from |
| 347 |
– |
Smith's early work on multipoles for the Ewald |
| 348 |
– |
summation.\cite{Smith82,Smith98} |
| 349 |
– |
|
| 350 |
– |
Note that increasing the value of $n$ will add additional terms to the |
| 351 |
– |
electrostatic potential, e.g., $f_2(r)$ includes orders up to |
| 352 |
– |
$(r-R_c)^3/R_c^4$, and so on. Successive derivatives of the $f_n(r)$ |
| 353 |
– |
functions are denoted $g_2(r) = f^\prime_2(r)$, $h_2(r) = |
| 354 |
– |
f^{\prime\prime}_2(r)$, etc. These higher derivatives are required |
| 355 |
– |
for computing multipole energies, forces, and torques, and smooth |
| 356 |
– |
cutoffs of these quantities can be guaranteed as long as the number of |
| 357 |
– |
terms in the Taylor series exceeds the derivative order required. |
| 358 |
– |
|
| 337 |
|
For multipole-multipole interactions, following this procedure results |
| 338 |
< |
in separate radial functions for each distinct orientational |
| 339 |
< |
contribution to the potential, and ensures that the forces and torques |
| 340 |
< |
from {\it each} of these contributions will vanish at the cutoff |
| 341 |
< |
radius. For example, the direct dipole dot product ($\mathbf{D}_{i} |
| 342 |
< |
\cdot \mathbf{D}_{j}$) is treated differently than the dipole-distance |
| 338 |
> |
in separate radial functions for each of the distinct orientational |
| 339 |
> |
contributions to the potential, and ensures that the forces and |
| 340 |
> |
torques from each of these contributions will vanish at the cutoff |
| 341 |
> |
radius. For example, the direct dipole dot product |
| 342 |
> |
($\mathbf{D}_{a} |
| 343 |
> |
\cdot \mathbf{D}_{b}$) is treated differently than the dipole-distance |
| 344 |
|
dot products: |
| 345 |
|
\begin{equation} |
| 346 |
< |
U_{D_{i}D_{j}}(r)= -\frac{1}{4\pi \epsilon_0} \left( \mathbf{D}_{i} \cdot |
| 347 |
< |
\mathbf{D}_{j} \right) \frac{g_2(r)}{r} |
| 348 |
< |
-\frac{1}{4\pi \epsilon_0} |
| 349 |
< |
\left( \mathbf{D}_{i} \cdot \hat{r} \right) |
| 350 |
< |
\left( \mathbf{D}_{j} \cdot \hat{r} \right) \left(h_2(r) - |
| 372 |
< |
\frac{g_2(r)}{r} \right) |
| 346 |
> |
U_{\mathbf{D}_{a}\mathbf{D}_{b}}(r)= -\frac{1}{4\pi \epsilon_0} \left[ \left( |
| 347 |
> |
\mathbf{D}_{a} \cdot |
| 348 |
> |
\mathbf{D}_{b} \right) v_{21}(r) + |
| 349 |
> |
\left( \mathbf{D}_{a} \cdot \hat{\mathbf{r}} \right) |
| 350 |
> |
\left( \mathbf{D}_{b} \cdot \hat{\mathbf{r}} \right) v_{22}(r) \right] |
| 351 |
|
\end{equation} |
| 352 |
|
|
| 353 |
< |
The electrostatic forces and torques acting on the central multipole |
| 354 |
< |
site due to another site within cutoff sphere are derived from |
| 353 |
> |
For the Taylor shifted (TSF) method with the undamped kernel, |
| 354 |
> |
$v_{21}(r) = -\frac{1}{r^3} + \frac{3 r}{r_c^4} - \frac{8}{r_c^3} + |
| 355 |
> |
\frac{6}{r r_c^2}$ and $v_{22}(r) = \frac{3}{r^3} + \frac{3 r}{r_c^4} |
| 356 |
> |
- \frac{6}{r r_c^2}$. In these functions, one can easily see the |
| 357 |
> |
connection to unmodified electrostatics as well as the smooth |
| 358 |
> |
transition to zero in both these functions as $r\rightarrow r_c$. The |
| 359 |
> |
electrostatic forces and torques acting on the central multipole due |
| 360 |
> |
to another site within the cutoff sphere are derived from |
| 361 |
|
Eq.~\ref{generic}, accounting for the appropriate number of |
| 362 |
|
derivatives. Complete energy, force, and torque expressions are |
| 363 |
|
presented in the first paper in this series (Reference |
| 364 |
< |
\citep{PaperI}). |
| 364 |
> |
\onlinecite{PaperI}). |
| 365 |
|
|
| 366 |
|
\subsection{Gradient-shifted force (GSF)} |
| 367 |
|
|
| 368 |
< |
A second (and significantly simpler) method involves shifting the |
| 369 |
< |
gradient of the raw coulomb potential for each particular multipole |
| 368 |
> |
A second (and conceptually simpler) method involves shifting the |
| 369 |
> |
gradient of the raw Coulomb potential for each particular multipole |
| 370 |
|
order. For example, the raw dipole-dipole potential energy may be |
| 371 |
|
shifted smoothly by finding the gradient for two interacting dipoles |
| 372 |
|
which have been projected onto the surface of the cutoff sphere |
| 373 |
|
without changing their relative orientation, |
| 374 |
< |
\begin{displaymath} |
| 375 |
< |
U_{D_{i}D_{j}}(r_{ij}) = U_{D_{i}D_{j}}(r_{ij}) - U_{D_{i}D_{j}}(R_c) |
| 376 |
< |
- (r_{ij}-R_c) \hat{r}_{ij} \cdot |
| 377 |
< |
\vec{\nabla} V_{D_{i}D_{j}}(r) \Big \lvert _{R_c} |
| 378 |
< |
\end{displaymath} |
| 379 |
< |
Here the lab-frame orientations of the two dipoles, $\mathbf{D}_{i}$ |
| 380 |
< |
and $\mathbf{D}_{j}$, are retained at the cutoff distance (although |
| 381 |
< |
the signs are reversed for the dipole that has been projected onto the |
| 382 |
< |
cutoff sphere). In many ways, this simpler approach is closer in |
| 383 |
< |
spirit to the original shifted force method, in that it projects a |
| 384 |
< |
neutralizing multipole (and the resulting forces from this multipole) |
| 385 |
< |
onto a cutoff sphere. The resulting functional forms for the |
| 386 |
< |
potentials, forces, and torques turn out to be quite similar in form |
| 387 |
< |
to the Taylor-shifted approach, although the radial contributions are |
| 388 |
< |
significantly less perturbed by the Gradient-shifted approach than |
| 389 |
< |
they are in the Taylor-shifted method. |
| 374 |
> |
\begin{equation} |
| 375 |
> |
U_{\mathbf{D}_{a}\mathbf{D}_{b}}(r) = U_{\mathbf{D}_{a}\mathbf{D}_{b}}(r) - |
| 376 |
> |
U_{\mathbf{D}_{a}\mathbf{D}_{b}}(r_c) |
| 377 |
> |
- (r_{ab}-r_c) ~~~\hat{\mathbf{r}}_{ab} \cdot |
| 378 |
> |
\nabla U_{\mathbf{D}_{a}\mathbf{D}_{b}}(r_c). |
| 379 |
> |
\end{equation} |
| 380 |
> |
Here the lab-frame orientations of the two dipoles, $\mathbf{D}_{a}$ and $\mathbf{D}_{b}$, are retained at the cutoff distance |
| 381 |
> |
(although the signs are reversed for the dipole that has been |
| 382 |
> |
projected onto the cutoff sphere). In many ways, this simpler |
| 383 |
> |
approach is closer in spirit to the original shifted force method, in |
| 384 |
> |
that it projects a neutralizing multipole (and the resulting forces |
| 385 |
> |
from this multipole) onto a cutoff sphere. The resulting functional |
| 386 |
> |
forms for the potentials, forces, and torques turn out to be quite |
| 387 |
> |
similar in form to the Taylor-shifted approach, although the radial |
| 388 |
> |
contributions are significantly less perturbed by the gradient-shifted |
| 389 |
> |
approach than they are in the Taylor-shifted method. |
| 390 |
> |
|
| 391 |
> |
For the gradient shifted (GSF) method with the undamped kernel, |
| 392 |
> |
$v_{21}(r) = -\frac{1}{r^3} - \frac{3 r}{r_c^4} + \frac{4}{r_c^3}$ and |
| 393 |
> |
$v_{22}(r) = \frac{3}{r^3} + \frac{9 r}{r_c^4} - \frac{12}{r_c^3}$. |
| 394 |
> |
Again, these functions go smoothly to zero as $r\rightarrow r_c$, and |
| 395 |
> |
because the Taylor expansion retains only one term, they are |
| 396 |
> |
significantly less perturbed than the TSF functions. |
| 397 |
|
|
| 398 |
|
In general, the gradient shifted potential between a central multipole |
| 399 |
|
and any multipolar site inside the cutoff radius is given by, |
| 400 |
|
\begin{equation} |
| 401 |
< |
U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) - |
| 402 |
< |
U(\mathbf{r}_c,\hat{\mathbf{a}}, \hat{\mathbf{b}}) - (r-r_c) \hat{r} |
| 403 |
< |
\cdot \nabla U(\mathbf{r},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \Big \lvert _{r_c} \right] |
| 401 |
> |
U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \mathsf{A}, \mathsf{B}) - |
| 402 |
> |
U(r_c \hat{\mathbf{r}},\mathsf{A}, \mathsf{B}) - (r-r_c) |
| 403 |
> |
\hat{\mathbf{r}} \cdot \nabla U(r_c \hat{\mathbf{r}},\mathsf{A}, \mathsf{B}) \right] |
| 404 |
|
\label{generic2} |
| 405 |
|
\end{equation} |
| 406 |
|
where the sum describes a separate force-shifting that is applied to |
| 407 |
< |
each orientational contribution to the energy. |
| 407 |
> |
each orientational contribution to the energy. In this expression, |
| 408 |
> |
$\hat{\mathbf{r}}$ is the unit vector connecting the two multipoles |
| 409 |
> |
($a$ and $b$) in space, and $\mathsf{A}$ and $\mathsf{B}$ |
| 410 |
> |
represent the orientations the multipoles. |
| 411 |
|
|
| 412 |
|
The third term converges more rapidly than the first two terms as a |
| 413 |
|
function of radius, hence the contribution of the third term is very |
| 414 |
|
small for large cutoff radii. The force and torque derived from |
| 415 |
< |
equation \ref{generic2} are consistent with the energy expression and |
| 416 |
< |
approach zero as $r \rightarrow R_c$. Both the GSF and TSF methods |
| 415 |
> |
Eq. \ref{generic2} are consistent with the energy expression and |
| 416 |
> |
approach zero as $r \rightarrow r_c$. Both the GSF and TSF methods |
| 417 |
|
can be considered generalizations of the original DSF method for |
| 418 |
|
higher order multipole interactions. GSF and TSF are also identical up |
| 419 |
|
to the charge-dipole interaction but generate different expressions in |
| 420 |
|
the energy, force and torque for higher order multipole-multipole |
| 421 |
|
interactions. Complete energy, force, and torque expressions for the |
| 422 |
|
GSF potential are presented in the first paper in this series |
| 423 |
< |
(Reference \citep{PaperI}) |
| 423 |
> |
(Reference~\onlinecite{PaperI}). |
| 424 |
|
|
| 425 |
|
|
| 426 |
|
\subsection{Shifted potential (SP) } |
| 433 |
|
interactions with the central multipole and the image. This |
| 434 |
|
effectively shifts the total potential to zero at the cutoff radius, |
| 435 |
|
\begin{equation} |
| 436 |
< |
U_{SP}(\vec r)=\sum U(\vec r) - U(\vec r_c) |
| 436 |
> |
U^{\text{SP}} = \sum \left[ U(\mathbf{r}, \mathsf{A}, \mathsf{B}) - |
| 437 |
> |
U(r_c \hat{\mathbf{r}},\mathsf{A}, \mathsf{B}) \right] |
| 438 |
|
\label{eq:SP} |
| 439 |
|
\end{equation} |
| 440 |
|
where the sum describes separate potential shifting that is done for |
| 441 |
|
each orientational contribution to the energy (e.g. the direct dipole |
| 442 |
|
product contribution is shifted {\it separately} from the |
| 443 |
|
dipole-distance terms in dipole-dipole interactions). Note that this |
| 444 |
< |
is not a simple shifting of the total potential at $R_c$. Each radial |
| 444 |
> |
is not a simple shifting of the total potential at $r_c$. Each radial |
| 445 |
|
contribution is shifted separately. One consequence of this is that |
| 446 |
|
multipoles that reorient after leaving the cutoff sphere can re-enter |
| 447 |
|
the cutoff sphere without perturbing the total energy. |
| 448 |
|
|
| 449 |
< |
The potential energy between a central multipole and other multipolar |
| 450 |
< |
sites then goes smoothly to zero as $r \rightarrow R_c$. However, the |
| 451 |
< |
force and torque obtained from the shifted potential (SP) are |
| 452 |
< |
discontinuous at $R_c$. Therefore, MD simulations will still |
| 453 |
< |
experience energy drift while operating under the SP potential, but it |
| 454 |
< |
may be suitable for Monte Carlo approaches where the configurational |
| 455 |
< |
energy differences are the primary quantity of interest. |
| 449 |
> |
For the shifted potential (SP) method with the undamped kernel, |
| 450 |
> |
$v_{21}(r) = -\frac{1}{r^3} + \frac{1}{r_c^3}$ and $v_{22}(r) = |
| 451 |
> |
\frac{3}{r^3} - \frac{3}{r_c^3}$. The potential energy between a |
| 452 |
> |
central multipole and other multipolar sites goes smoothly to zero as |
| 453 |
> |
$r \rightarrow r_c$. However, the force and torque obtained from the |
| 454 |
> |
shifted potential (SP) are discontinuous at $r_c$. MD simulations |
| 455 |
> |
will still experience energy drift while operating under the SP |
| 456 |
> |
potential, but it may be suitable for Monte Carlo approaches where the |
| 457 |
> |
configurational energy differences are the primary quantity of |
| 458 |
> |
interest. |
| 459 |
|
|
| 460 |
< |
\subsection{The Self term} |
| 460 |
> |
\subsection{The Self Term} |
| 461 |
|
In the TSF, GSF, and SP methods, a self-interaction is retained for |
| 462 |
|
the central multipole interacting with its own image on the surface of |
| 463 |
|
the cutoff sphere. This self interaction is nearly identical with the |
| 464 |
|
self-terms that arise in the Ewald sum for multipoles. Complete |
| 465 |
|
expressions for the self terms are presented in the first paper in |
| 466 |
< |
this series (Reference \citep{PaperI}) |
| 466 |
> |
this series (Reference \onlinecite{PaperI}). |
| 467 |
|
|
| 468 |
|
|
| 469 |
|
\section{\label{sec:methodology}Methodology} |
| 475 |
|
real-space cutoffs. In the first paper of this series, we compared |
| 476 |
|
the dipolar and quadrupolar energy expressions against analytic |
| 477 |
|
expressions for ordered dipolar and quadrupolar |
| 478 |
< |
arrays.\cite{Sauer,LT,Nagai01081960,Nagai01091963} This work uses the |
| 479 |
< |
multipolar Ewald sum as a reference method for comparing energies, |
| 480 |
< |
forces, and torques for molecular models that mimic disordered and |
| 481 |
< |
ordered condensed-phase systems. These test-cases include: |
| 478 |
> |
arrays.\cite{Sauer,LT,Nagai01081960,Nagai01091963} In this work, we |
| 479 |
> |
used the multipolar Ewald sum as a reference method for comparing |
| 480 |
> |
energies, forces, and torques for molecular models that mimic |
| 481 |
> |
disordered and ordered condensed-phase systems. The parameters used |
| 482 |
> |
in the test cases are given in table~\ref{tab:pars}. |
| 483 |
|
|
| 484 |
< |
\begin{itemize} |
| 485 |
< |
\item Soft Dipolar fluids ($\sigma = , \epsilon = , |D| = $) |
| 486 |
< |
\item Soft Dipolar solids ($\sigma = , \epsilon = , |D| = $) |
| 487 |
< |
\item Soft Quadrupolar fluids ($\sigma = , \epsilon = , Q_{xx} = ...$) |
| 488 |
< |
\item Soft Quadrupolar solids ($\sigma = , \epsilon = , Q_{xx} = ...$) |
| 489 |
< |
\item A mixed multipole model for water |
| 490 |
< |
\item A mixed multipole models for water with dissolved ions |
| 491 |
< |
\end{itemize} |
| 492 |
< |
This last test case exercises all levels of the multipole-multipole |
| 493 |
< |
interactions we have derived so far and represents the most complete |
| 494 |
< |
test of the new methods. |
| 484 |
> |
\begin{table} |
| 485 |
> |
\caption{The parameters used in the systems used to evaluate the new |
| 486 |
> |
real-space methods. The most comprehensive test was a liquid |
| 487 |
> |
composed of 2000 soft DQ liquid molecules with 48 dissolved ions (24 \ce{Na+} and 24 \ce{Cl-} |
| 488 |
> |
ions). This test exercises all orders of the multipolar |
| 489 |
> |
interactions developed in the first paper.\label{tab:pars}} |
| 490 |
> |
\begin{tabularx}{\textwidth}{r|cc|YYccc|Yccc} \hline |
| 491 |
> |
& \multicolumn{2}{c|}{LJ parameters} & |
| 492 |
> |
\multicolumn{5}{c|}{Electrostatic moments} & & & & \\ |
| 493 |
> |
Test system & $\sigma$& $\epsilon$ & $C$ & $D$ & |
| 494 |
> |
$Q_{xx}$ & $Q_{yy}$ & $Q_{zz}$ & mass & $I_{xx}$ & $I_{yy}$ & |
| 495 |
> |
$I_{zz}$ \\ \cline{6-8}\cline{10-12} |
| 496 |
> |
& (\AA) & (kcal/mol) & (e) & (debye) & \multicolumn{3}{c|}{(debye \AA)} & (amu) & \multicolumn{3}{c}{(amu |
| 497 |
> |
\AA\textsuperscript{2})} \\ \hline |
| 498 |
> |
Soft Dipolar fluid & 3.051 & 0.152 & & 2.35 & & & & 18.0153 & 1.77&0.6145& 1.155 \\ |
| 499 |
> |
Soft Dipolar solid & 2.837 & 1.0 & & 2.35 & & & & $10^4$ & 17.6 &17.6 & 0 \\ |
| 500 |
> |
Soft Quadrupolar fluid & 3.051 & 0.152 & & & -1&-1&-2.5 & 18.0153 & 1.77&0.6145&1.155 \\ |
| 501 |
> |
Soft Quadrupolar solid & 2.837 & 1.0 & & & -1&-1&-2.5 & $10^4$ & 17.6&17.6&0 \\ |
| 502 |
> |
Soft DQ liquid & 3.051 & 0.152 & & 2.35 & -1.35&0&-0.68 & 18.0153 & 1.77&0.6145&1.155 \\ |
| 503 |
> |
\ce{Na+} & 2.579 & 0.118 & +1& & & & & 22.99 & & &\\ |
| 504 |
> |
\ce{Cl-} & 4.445 & 0.1 & -1& & & & & 35.4527& & & \\ \hline |
| 505 |
> |
\end{tabularx} |
| 506 |
> |
\end{table} |
| 507 |
> |
The systems consist of pure multipolar solids (both dipole and |
| 508 |
> |
quadrupole), pure multipolar liquids (both dipole and quadrupole), a |
| 509 |
> |
fluid composed of sites containing both dipoles and quadrupoles |
| 510 |
> |
simultaneously, and a final test case that includes ions with point |
| 511 |
> |
charges in addition to the multipolar fluid. The solid-phase |
| 512 |
> |
parameters were chosen so that the systems can explore some |
| 513 |
> |
orientational freedom for the multipolar sites, while maintaining |
| 514 |
> |
relatively strict translational order. The soft DQ liquid model used |
| 515 |
> |
here based loosely on the SSDQO water |
| 516 |
> |
model,\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} but is not itself a |
| 517 |
> |
particularly accurate water model. However, the soft DQ model does |
| 518 |
> |
test dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole |
| 519 |
> |
interactions at roughly the same magnitudes. The last test case, a |
| 520 |
> |
soft DQ liquid with dissolved ions, exercises \textit{all} levels of |
| 521 |
> |
the multipole-multipole interactions we have derived so far and |
| 522 |
> |
represents the most complete test of the new methods. |
| 523 |
|
|
| 524 |
|
In the following section, we present results for the total |
| 525 |
|
electrostatic energy, as well as the electrostatic contributions to |
| 526 |
|
the force and torque on each molecule. These quantities have been |
| 527 |
|
computed using the SP, TSF, and GSF methods, as well as a hard cutoff, |
| 528 |
< |
and have been compared with the values obtaine from the multipolar |
| 529 |
< |
Ewald sum. In Mote Carlo (MC) simulations, the energy differences |
| 528 |
> |
and have been compared with the values obtained from the multipolar |
| 529 |
> |
Ewald sum. In Monte Carlo (MC) simulations, the energy differences |
| 530 |
|
between two configurations is the primary quantity that governs how |
| 531 |
< |
the simulation proceeds. These differences are the most imporant |
| 531 |
> |
the simulation proceeds. These differences are the most important |
| 532 |
|
indicators of the reliability of a method even if the absolute |
| 533 |
|
energies are not exact. For each of the multipolar systems listed |
| 534 |
|
above, we have compared the change in electrostatic potential energy |
| 537 |
|
behavior of the simulation, so we also compute the electrostatic |
| 538 |
|
contributions to the forces and torques. |
| 539 |
|
|
| 540 |
< |
\subsection{Model systems} |
| 541 |
< |
To sample independent configurations of multipolar crystals, a body |
| 542 |
< |
centered cubic (BCC) crystal which is a minimum energy structure for |
| 543 |
< |
point dipoles was generated using 3,456 molecules. The multipoles |
| 544 |
< |
were translationally locked in their respective crystal sites for |
| 545 |
< |
equilibration at a relatively low temperature (50K), so that dipoles |
| 546 |
< |
or quadrupoles could freely explore all accessible orientations. The |
| 547 |
< |
translational constraints were removed, and the crystals were |
| 521 |
< |
simulated for 10 ps in the microcanonical (NVE) ensemble with an |
| 522 |
< |
average temperature of 50 K. Configurations were sampled at equal |
| 523 |
< |
time intervals for the comparison of the configurational energy |
| 524 |
< |
differences. The crystals were not simulated close to the melting |
| 525 |
< |
points in order to avoid translational deformation away of the ideal |
| 526 |
< |
lattice geometry. |
| 540 |
> |
\subsection{Implementation} |
| 541 |
> |
The real-space methods developed in the first paper in this series |
| 542 |
> |
have been implemented in our group's open source molecular simulation |
| 543 |
> |
program, OpenMD,\cite{Meineke05,openmd} which was used for all calculations in |
| 544 |
> |
this work. The complementary error function can be a relatively slow |
| 545 |
> |
function on some processors, so all of the radial functions are |
| 546 |
> |
precomputed on a fine grid and are spline-interpolated to provide |
| 547 |
> |
values when required. |
| 548 |
|
|
| 549 |
< |
For dipolar, quadrupolar, and mixed-multipole liquid simulations, each |
| 550 |
< |
system was created with 2048 molecules oriented randomly. These were |
| 549 |
> |
Using the same simulation code, we compare to a multipolar Ewald sum |
| 550 |
> |
with a reciprocal space cutoff, $k_\mathrm{max} = 7$. Our version of |
| 551 |
> |
the Ewald sum is a re-implementation of the algorithm originally |
| 552 |
> |
proposed by Smith that does not use the particle mesh or smoothing |
| 553 |
> |
approximations.\cite{Smith82,Smith98} This implementation was tested |
| 554 |
> |
extensively against the analytic energy constants for the multipolar |
| 555 |
> |
lattices that are discussed in reference \onlinecite{PaperI}. In all |
| 556 |
> |
cases discussed below, the quantities being compared are the |
| 557 |
> |
electrostatic contributions to energies, force, and torques. All |
| 558 |
> |
other contributions to these quantities (i.e. from Lennard-Jones |
| 559 |
> |
interactions) are removed prior to the comparisons. |
| 560 |
|
|
| 561 |
< |
system with 2,048 molecules simulated for 1ns in NVE ensemble at 300 K |
| 562 |
< |
temperature after equilibration. We collected 250 different |
| 563 |
< |
configurations in equal interval of time. For the ions mixed liquid |
| 564 |
< |
system, we converted 48 different molecules into 24 \ce{Na+} and 24 |
| 565 |
< |
\ce{Cl-} ions and equilibrated. After equilibration, the system was run |
| 566 |
< |
at the same environment for 1ns and 250 configurations were |
| 567 |
< |
collected. While comparing energies, forces, and torques with Ewald |
| 568 |
< |
method, Lennard-Jones potentials were turned off and purely |
| 569 |
< |
electrostatic interaction had been compared. |
| 561 |
> |
The convergence parameter ($\alpha$) also plays a role in the balance |
| 562 |
> |
of the real-space and reciprocal-space portions of the Ewald |
| 563 |
> |
calculation. Typical molecular mechanics packages set this to a value |
| 564 |
> |
that depends on the cutoff radius and a tolerance (typically less than |
| 565 |
> |
$1 \times 10^{-4}$ kcal/mol). Smaller tolerances are typically |
| 566 |
> |
associated with increasing accuracy at the expense of computational |
| 567 |
> |
time spent on the reciprocal-space portion of the |
| 568 |
> |
summation.\cite{Perram88,Essmann:1995pb} A default tolerance of $1 \times |
| 569 |
> |
10^{-8}$ kcal/mol was used in all Ewald calculations, resulting in |
| 570 |
> |
Ewald coefficient 0.3119 \AA$^{-1}$ for a cutoff radius of 12 \AA. |
| 571 |
|
|
| 572 |
+ |
The real-space models have self-interactions that provide |
| 573 |
+ |
contributions to the energies only. Although the self interaction is |
| 574 |
+ |
a rapid calculation, we note that in systems with fluctuating charges |
| 575 |
+ |
or point polarizabilities, the self-term is not static and must be |
| 576 |
+ |
recomputed at each time step. |
| 577 |
+ |
|
| 578 |
+ |
\subsection{Model systems} |
| 579 |
+ |
To sample independent configurations of the multipolar crystals, body |
| 580 |
+ |
centered cubic (bcc) crystals, which exhibit the minimum energy |
| 581 |
+ |
structures for point dipoles, were generated using 3,456 molecules. |
| 582 |
+ |
The multipoles were translationally locked in their respective crystal |
| 583 |
+ |
sites for equilibration at a relatively low temperature (50K) so that |
| 584 |
+ |
dipoles or quadrupoles could freely explore all accessible |
| 585 |
+ |
orientations. The translational constraints were then removed, the |
| 586 |
+ |
systems were re-equilibrated, and the crystals were simulated for an |
| 587 |
+ |
additional 10 ps in the microcanonical (NVE) ensemble with an average |
| 588 |
+ |
temperature of 50 K. The balance between moments of inertia and |
| 589 |
+ |
particle mass were chosen to allow orientational sampling without |
| 590 |
+ |
significant translational motion. Configurations were sampled at |
| 591 |
+ |
equal time intervals in order to compare configurational energy |
| 592 |
+ |
differences. The crystals were simulated far from the melting point |
| 593 |
+ |
in order to avoid translational deformation away of the ideal lattice |
| 594 |
+ |
geometry. |
| 595 |
+ |
|
| 596 |
+ |
For dipolar, quadrupolar, and mixed-multipole \textit{liquid} |
| 597 |
+ |
simulations, each system was created with 2,048 randomly-oriented |
| 598 |
+ |
molecules. These were equilibrated at a temperature of 300K for 1 ns. |
| 599 |
+ |
Each system was then simulated for 1 ns in the microcanonical (NVE) |
| 600 |
+ |
ensemble with the Dullweber, Leimkuhler, and McLachlan (DLM) |
| 601 |
+ |
symplectic splitting integrator using 1 fs |
| 602 |
+ |
timesteps.\cite{Dullweber1997} We collected 250 different |
| 603 |
+ |
configurations at equal time intervals. For the liquid system that |
| 604 |
+ |
included ionic species, we converted 48 randomly-distributed molecules |
| 605 |
+ |
into 24 \ce{Na+} and 24 \ce{Cl-} ions and re-equilibrated. After |
| 606 |
+ |
equilibration, the system was run under the same conditions for 1 |
| 607 |
+ |
ns. A total of 250 configurations were collected. In the following |
| 608 |
+ |
comparisons of energies, forces, and torques, the Lennard-Jones |
| 609 |
+ |
potentials were turned off and only the purely electrostatic |
| 610 |
+ |
quantities were compared with the same values obtained via the Ewald |
| 611 |
+ |
sum. |
| 612 |
+ |
|
| 613 |
|
\subsection{Accuracy of Energy Differences, Forces and Torques} |
| 614 |
|
The pairwise summation techniques (outlined above) were evaluated for |
| 615 |
|
use in MC simulations by studying the energy differences between |
| 622 |
|
should be identical for all methods. |
| 623 |
|
|
| 624 |
|
Since none of the real-space methods provide exact energy differences, |
| 625 |
< |
we used least square regressions analysiss for the six different |
| 625 |
> |
we used least square regressions analysis for the six different |
| 626 |
|
molecular systems to compare $\Delta E$ from Hard, SP, GSF, and TSF |
| 627 |
< |
with the multipolar Ewald reference method. Unitary results for both |
| 628 |
< |
the correlation (slope) and correlation coefficient for these |
| 629 |
< |
regressions indicate perfect agreement between the real-space method |
| 630 |
< |
and the multipolar Ewald sum. |
| 627 |
> |
with the multipolar Ewald reference method. A result of unity for |
| 628 |
> |
both the correlation (slope) and coefficient of determination ($R^2$) |
| 629 |
> |
for these regressions would indicate perfect agreement between the |
| 630 |
> |
real-space method and the multipolar Ewald sum. |
| 631 |
|
|
| 632 |
|
Molecular systems were run long enough to explore independent |
| 633 |
|
configurations and 250 configurations were recorded for comparison. |
| 634 |
|
Each system provided 31,125 energy differences for a total of 186,750 |
| 635 |
|
data points. Similarly, the magnitudes of the forces and torques have |
| 636 |
< |
also been compared by using least squares regression analyses. In the |
| 636 |
> |
also been compared using least squares regression analysis. In the |
| 637 |
|
forces and torques comparison, the magnitudes of the forces acting in |
| 638 |
|
each molecule for each configuration were evaluated. For example, our |
| 639 |
|
dipolar liquid simulation contains 2048 molecules and there are 250 |
| 646 |
|
simulations. Because the real space methods reweight the different |
| 647 |
|
orientational contributions to the energies, it is also important to |
| 648 |
|
understand how the methods impact the \textit{directionality} of the |
| 649 |
< |
force and torque vectors. Fisher developed a probablity density |
| 649 |
> |
force and torque vectors. Fisher developed a probability density |
| 650 |
|
function to analyse directional data sets, |
| 651 |
|
\begin{equation} |
| 652 |
|
p_f(\theta) = \frac{\kappa}{2 \sinh\kappa}\sin\theta e^{\kappa \cos\theta} |
| 660 |
|
the forces obtained via the Ewald sum and the real-space methods were |
| 661 |
|
evaluated, |
| 662 |
|
\begin{equation} |
| 663 |
< |
\cos\theta_i = \frac{\vec{f}_i^\mathrm{~Ewald} \cdot |
| 664 |
< |
\vec{f}_i^\mathrm{~GSF}}{\left|\vec{f}_i^\mathrm{~Ewald}\right| \left|\vec{f}_i^\mathrm{~GSF}\right|} |
| 663 |
> |
\cos\theta_i = \frac{\mathbf{f}_i^\mathrm{~Ewald} \cdot |
| 664 |
> |
\mathbf{f}_i^\mathrm{~GSF}}{\left|\mathbf{f}_i^\mathrm{~Ewald}\right| \left|\mathbf{f}_i^\mathrm{~GSF}\right|} |
| 665 |
|
\end{equation} |
| 666 |
|
The total angular displacement of the vectors was calculated as, |
| 667 |
|
\begin{equation} |
| 684 |
|
|
| 685 |
|
\subsection{Energy conservation} |
| 686 |
|
To test conservation the energy for the methods, the mixed molecular |
| 687 |
< |
system of 2000 SSDQ water molecules with 24 \ce{Na+} and 24 \ce{Cl-} |
| 688 |
< |
ions was run for 1 ns in the microcanonical ensemble at an average |
| 689 |
< |
temperature of 300K. Each of the different electrostatic methods |
| 690 |
< |
(Ewald, Hard, SP, GSF, and TSF) was tested for a range of different |
| 691 |
< |
damping values. The molecular system was started with same initial |
| 692 |
< |
positions and velocities for all cutoff methods. The energy drift |
| 693 |
< |
($\delta E_1$) and standard deviation of the energy about the slope |
| 694 |
< |
($\delta E_0$) were evaluated from the total energy of the system as a |
| 695 |
< |
function of time. Although both measures are valuable at |
| 687 |
> |
system of 2000 soft DQ liquid molecules with 24 \ce{Na+} and 24 |
| 688 |
> |
\ce{Cl-} ions was run for 1 ns in the microcanonical ensemble at an |
| 689 |
> |
average temperature of 300K. Each of the different electrostatic |
| 690 |
> |
methods (Ewald, Hard, SP, GSF, and TSF) was tested for a range of |
| 691 |
> |
different damping values. The molecular system was started with same |
| 692 |
> |
initial positions and velocities for all cutoff methods. The energy |
| 693 |
> |
drift ($\delta E_1$) and standard deviation of the energy about the |
| 694 |
> |
slope ($\delta E_0$) were evaluated from the total energy of the |
| 695 |
> |
system as a function of time. Although both measures are valuable at |
| 696 |
|
investigating new methods for molecular dynamics, a useful interaction |
| 697 |
|
model must allow for long simulation times with minimal energy drift. |
| 698 |
|
|
| 699 |
|
\section{\label{sec:result}RESULTS} |
| 700 |
|
\subsection{Configurational energy differences} |
| 701 |
< |
%The magnitude of the fluctuation in the total electrostatic energy per molecule for a dipolar crystal is very high as shown in (Fig … paper I).\cite{PaperI}As soon as, the net dipole moment within a cutoff radius is neutralized in the SP method, the magnitude of the fluctuation in the total electrostatic energy per molecule reduced significantly and rapidly converged to the correct energy constant (Refer figure … Paper I).\cite{PaperI} The GSF potential energy also converged to the correct energy constant for the cutoff radius rc = 6a for the undamped case. The potential energy from the TSF method converges towards the correct value for a very large cutoff radius. The speed of convergence for the all the cutoff methods can be increased by using damping function as shown in figure … Paper I\cite{PaperI}. For the quadrupolar crystals, the fluctuation in the total electrostatic energy for the hard cutoff method is small and short ranged as compared to the dipolar crystals (figure … in the paper I).\cite{PaperI} Similar to the dipolar crystals, the net quadrupolar neutralization of the cutoff sphere in the SP method reduces oscillation rapidly and converge electrostatic energy to the correct energy constant. |
| 630 |
< |
%The oscillation in the the electrostatic energy for the hard cutoff method is even true for the dipolar liquids as shown in Figure ~\ref{fig:rcutConvergence_dipolarLiquid}. As we placed image on the surface of the cutoff sphere in SP method, the oscillation in the energy is reduced. The fluctuation in the energy in liquid is much smaller as compared to the crystal (This result is similar to the results observed by \textit{Wolf et al.} in the case of ionic crystal and Mgo melt). The large magnitude in the fluctuation of the electrostatic energy in the crystal is because of large range of multipole ordering in the crystal. When the energy is evaluated by the direct truncation, it breaks up large number of multipolar ordering leaving behind net multipole moment. But in the case of liquid, there is only local ordering of the multipoles and their ordering disappears in the long range. Therefore, the direct truncation results a small oscillation in the electrostatic energy (which is smaller than deviation SP energy from the Ewald Figure ~\ref{fig:rcutConvergence_dipolarLiquid}) in the case of liquid. Although, the oscillation in the energy is very small for the case of liquid, this affects the change in potential energy ($\triangle E$), which is observed when $\triangle E$ evaluated from the SP method compared with Ewald as shown in figure 4a and 4b. |
| 631 |
< |
%\begin{figure}[h!] |
| 632 |
< |
% \centering |
| 633 |
< |
% \includegraphics[width=0.50 \textwidth]{rcutConvergence_dipolarLiquid-crop.pdf} |
| 634 |
< |
% \caption{The energy per molecule plotted against cutoff radius, rc for i) Hard ii) SP iii) GSF, and iv) TSF method. The hard cutoff method shows fluctuation in the electorstatic energy and it disappers in all other methods. } |
| 635 |
< |
% \label{fig:rcutConvergence_dipolarLiquid} |
| 636 |
< |
% \end{figure} |
| 637 |
< |
%In MC simulations, the electrostatic differences between the molecules are important parameter for sampling. We have compared $\triangle E$ from the different methods (Hard, SP, GSF, and TSF) with the Ewald using linear regression analysis. The correlation coefficient ($R^2$) of the regression line measures the deviation of the evaluated quantities from the mean slope. We know that Ewald method evaluates accurate value of the electrostatic energy. Hence, if the proposed methods can quantify the electrostatic energy as good as Ewald then the correlation coefficient is 1.The correlation coefficient is 0 for the completely random result for any physical quantity measured by the proposed method. The slope is a measure of the accuracy of the average of a physical quantity obtained from the proposed methods. If the slope is 1 then we can conclude that the average of the physical quantity measured by the method is as good as Ewald. The deviation of the slope from 1 state that the method used in quantifying physical quantities is statistically biased as compared to Ewald. |
| 638 |
< |
%\begin{figure} |
| 639 |
< |
% \centering |
| 640 |
< |
% \includegraphics[width=0.45 \textwidth]{slopeComparision_undamped.pdf} |
| 641 |
< |
% \label{fig:barGraph1} |
| 642 |
< |
% \end{figure} |
| 643 |
< |
% \begin{figure} |
| 644 |
< |
% \centering |
| 645 |
< |
% \includegraphics[width=0.45 \textwidth]{slopeComparision_undamped.pdf} |
| 646 |
< |
% \caption{} |
| 647 |
< |
|
| 648 |
< |
% \label{fig:barGraph2} |
| 649 |
< |
% \end{figure} |
| 650 |
< |
%The correlation coefficient ($R^2$) and slope of the linear regression plots for the energy differences for all six different molecular systems is shown in figure 4a and 4b.The plot shows that the correlation coefficient improves for the SP cutoff method as compared to the undamped hard cutoff method in the case of SSDQC, SSDQ, dipolar crystal, and dipolar liquid. For the quadrupolar crystal and liquid, the correlation coefficient is almost unchanged and close to 1. The correlation coefficient is smallest (0.696276 for $r_c$ = 9 $A^o$) for the SSDQC liquid because of the presence of charge-charge and charge-multipole interactions. Since the charge-charge and charge-multipole interaction is long ranged, there is huge deviation of correlation coefficient from 1. Similarly, the quarupole–quadrupole interaction is short ranged ($\sim 1/r^6$) with compared to interactions in the other multipolar systems, thus the correlation coefficient very close to 1 even for hard cutoff method. The idea of placing image multipole on the surface of the cutoff sphere improves the correlation coefficient and makes it close to 1 for all types of multipolar systems. Similarly the slope is hugely deviated from the correct value for the lower order multipole-multipole interaction and slightly deviated for higher order multipole – multipole interaction. The SP method improves both correlation coefficient ($R^2$) and slope significantly in SSDQC and dipolar systems. The Slope is found to be deviated more in dipolar crystal as compared to liquid which is associated with the large fluctuation in the electrostatic energy in crystal. The GSF also produced better values of correlation coefficient and slope with the proper selection of the damping alpha (Interested reader can consult accompanying supporting material). The TSF method gives good value of correlation coefficient for the dipolar crystal, dipolar liquid, SSDQ, and SSDQC (not for the quadrupolar crystal and liquid) but the regression slopes are significantly deviated. |
| 701 |
> |
|
| 702 |
|
\begin{figure} |
| 703 |
< |
\centering |
| 704 |
< |
\includegraphics[width=0.50 \textwidth]{energyPlot_slopeCorrelation_combined-crop.pdf} |
| 705 |
< |
\caption{The correlation coefficient and regression slope of configurational energy differences for a given method with compared with the reference Ewald method. The value of result equal to 1(dashed line) indicates energy difference is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 \AA\ = circle, 12 \AA\ = square 15 \AA\ = inverted triangle)} |
| 706 |
< |
\label{fig:slopeCorr_energy} |
| 707 |
< |
\end{figure} |
| 708 |
< |
The combined correlation coefficient and slope for all six systems is shown in Figure ~\ref{fig:slopeCorr_energy}. The correlation coefficient for the undamped hard cutoff method is does not have good agreement with the Ewald because of the fluctuation of the electrostatic energy in the direct truncation method. This deviation in correlation coefficient is improved by using SP, GSF, and TSF method. But the TSF method worsens the regression slope stating that this method produces statistically more biased result as compared to Ewald. Also the GSF method slightly deviate slope but it can be alleviated by using proper value of damping alpha and cutoff radius. The SP method shows good agreement with Ewald method for all values of damping alpha and radii. |
| 703 |
> |
\centering |
| 704 |
> |
\includegraphics[width=0.6\linewidth]{energyPlot_slopeCorrelation_combined.eps} |
| 705 |
> |
\caption{Statistical analysis of the quality of configurational |
| 706 |
> |
energy differences for the real-space electrostatic methods |
| 707 |
> |
compared with the reference Ewald sum. Results with a value equal |
| 708 |
> |
to 1 (dashed line) indicate $\Delta E$ values indistinguishable |
| 709 |
> |
from those obtained using the multipolar Ewald sum. Different |
| 710 |
> |
values of the cutoff radius are indicated with different symbols |
| 711 |
> |
(9~\AA\ = circles, 12~\AA\ = squares, and 15~\AA\ = inverted |
| 712 |
> |
triangles).\label{fig:slopeCorr_energy}} |
| 713 |
> |
\end{figure} |
| 714 |
> |
|
| 715 |
> |
The combined coefficient of determination and slope for all six |
| 716 |
> |
systems is shown in Figure ~\ref{fig:slopeCorr_energy}. Most of the |
| 717 |
> |
methods reproduce the Ewald configurational energy differences with |
| 718 |
> |
remarkable fidelity. Undamped hard cutoffs introduce a significant |
| 719 |
> |
amount of random scatter in the energy differences which is apparent |
| 720 |
> |
in the reduced value of $R^2$ for this method. This can be easily |
| 721 |
> |
understood as configurations which exhibit small traversals of a few |
| 722 |
> |
dipoles or quadrupoles out of the cutoff sphere will see large energy |
| 723 |
> |
jumps when hard cutoffs are used. The orientations of the multipoles |
| 724 |
> |
(particularly in the ordered crystals) mean that these energy jumps |
| 725 |
> |
can go in either direction, producing a significant amount of random |
| 726 |
> |
scatter, but no systematic error. |
| 727 |
> |
|
| 728 |
> |
The TSF method produces energy differences that are highly correlated |
| 729 |
> |
with the Ewald results, but it also introduces a significant |
| 730 |
> |
systematic bias in the values of the energies, particularly for |
| 731 |
> |
smaller cutoff values. The TSF method alters the distance dependence |
| 732 |
> |
of different orientational contributions to the energy in a |
| 733 |
> |
non-uniform way, so the size of the cutoff sphere can have a large |
| 734 |
> |
effect, particularly for the crystalline systems. |
| 735 |
> |
|
| 736 |
> |
Both the SP and GSF methods appear to reproduce the Ewald results with |
| 737 |
> |
excellent fidelity, particularly for moderate damping ($\alpha \approx |
| 738 |
> |
0.2$~\AA$^{-1}$) and with a commonly-used cutoff value ($r_c = |
| 739 |
> |
12$~\AA). With the exception of the undamped hard cutoff, and the TSF |
| 740 |
> |
method with short cutoffs, all of the methods would be appropriate for |
| 741 |
> |
use in Monte Carlo simulations. |
| 742 |
> |
|
| 743 |
|
\subsection{Magnitude of the force and torque vectors} |
| 744 |
< |
The comparison of the magnitude of the combined forces and torques for the data accumulated from all system types are shown in Figure ~\ref{fig:slopeCorr_force}. The correlation and slope for the forces agree with the Ewald even for the hard cutoff method. For the system of molecules with higher order multipoles, the interaction is short ranged. Moreover, the force decays more rapidly than the electrostatic energy hence the hard cutoff method also produces good results. Although the pure cutoff gives the good match of the electrostatic force, the discontinuity in the force at the cutoff radius causes problem in the total energy conservation in MD simulations, which will be discussed in detail in subsection D. The correlation coefficient for GSF method also perfectly matches with Ewald but the slope is slightly deviated (due to extra term obtained from the angular differentiation). This deviation in the slope can be alleviated with proper selection of the damping alpha and radii ($\alpha = 0.2$ and $r_c = 12 A^o$ are good choice). The TSF method shows good agreement in the correlation coefficient but the slope is not good as compared to the Ewald. |
| 744 |
> |
|
| 745 |
> |
The comparisons of the magnitudes of the forces and torques for the |
| 746 |
> |
data accumulated from all six systems are shown in Figures |
| 747 |
> |
~\ref{fig:slopeCorr_force} and \ref{fig:slopeCorr_torque}. The |
| 748 |
> |
correlation and slope for the forces agree well with the Ewald sum |
| 749 |
> |
even for the hard cutoffs. |
| 750 |
> |
|
| 751 |
> |
For systems of molecules with only multipolar interactions, the pair |
| 752 |
> |
energy contributions are quite short ranged. Moreover, the force |
| 753 |
> |
decays more rapidly than the electrostatic energy, hence the hard |
| 754 |
> |
cutoff method can also produce reasonable agreement for this quantity. |
| 755 |
> |
Although the pure cutoff gives reasonably good electrostatic forces |
| 756 |
> |
for pairs of molecules included within each other's cutoff spheres, |
| 757 |
> |
the discontinuity in the force at the cutoff radius can potentially |
| 758 |
> |
cause energy conservation problems as molecules enter and leave the |
| 759 |
> |
cutoff spheres. This is discussed in detail in section |
| 760 |
> |
\ref{sec:conservation}. |
| 761 |
> |
|
| 762 |
> |
The two shifted-force methods (GSF and TSF) exhibit a small amount of |
| 763 |
> |
systematic variation and scatter compared with the Ewald forces. The |
| 764 |
> |
shifted-force models intentionally perturb the forces between pairs of |
| 765 |
> |
molecules inside each other's cutoff spheres in order to correct the |
| 766 |
> |
energy conservation issues, and this perturbation is evident in the |
| 767 |
> |
statistics accumulated for the molecular forces. The GSF |
| 768 |
> |
perturbations are minimal, particularly for moderate damping and |
| 769 |
> |
commonly-used cutoff values ($r_c = 12$~\AA). The TSF method shows |
| 770 |
> |
reasonable agreement in $R^2$, but again the systematic error in the |
| 771 |
> |
forces is concerning if replication of Ewald forces is desired. |
| 772 |
> |
|
| 773 |
> |
It is important to note that the forces and torques from the SP and |
| 774 |
> |
the Hard cutoffs are not identical. The SP method shifts each |
| 775 |
> |
orientational contribution separately (e.g. the dipole-dipole dot |
| 776 |
> |
product is shifted by a different function than the dipole-distance |
| 777 |
> |
products), while the hard cutoff contains no orientation-dependent |
| 778 |
> |
shifting. The forces and torques for these methods therefore diverge |
| 779 |
> |
for multipoles even though the forces for point charges are identical. |
| 780 |
> |
|
| 781 |
|
\begin{figure} |
| 782 |
< |
\centering |
| 783 |
< |
\includegraphics[width=0.50 \textwidth]{forcePlot_slopeCorrelation_combined-crop.pdf} |
| 784 |
< |
\caption{The correlation coefficient and regression slope of the magnitude of the force for a given method with compared to the reference Ewald method. The value of result equal to 1(dashed line) indicates, the magnitude of the force from a method is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 \AA\ = circle, 12 \AA\ = square 15 \AA\ = inverted triangle). } |
| 785 |
< |
\label{fig:slopeCorr_force} |
| 786 |
< |
\end{figure} |
| 787 |
< |
The torques appears to be very influenced because of extra term generated when the potential energy is modified to get consistent force and torque. The result shows that the torque from the hard cutoff method has good agreement with Ewald. As the potential is modified to make it consistent with the force and torque, the correlation and slope is deviated as shown in Figure~\ref{fig:slopeCorr_torque} for SP, GSF and TSF cutoff methods. But the proper value of the damping alpha and radius can improve the agreement of the GSF with the Ewald method. The TSF method shows worst agreement in the slope as compared to Ewald even for larger cutoff radii. |
| 782 |
> |
\centering |
| 783 |
> |
\includegraphics[width=0.6\linewidth]{forcePlot_slopeCorrelation_combined.eps} |
| 784 |
> |
\caption{Statistical analysis of the quality of the force vector |
| 785 |
> |
magnitudes for the real-space electrostatic methods compared with |
| 786 |
> |
the reference Ewald sum. Results with a value equal to 1 (dashed |
| 787 |
> |
line) indicate force magnitude values indistinguishable from those |
| 788 |
> |
obtained using the multipolar Ewald sum. Different values of the |
| 789 |
> |
cutoff radius are indicated with different symbols (9~\AA\ = |
| 790 |
> |
circles, 12~\AA\ = squares, and 15~\AA\ = inverted |
| 791 |
> |
triangles).\label{fig:slopeCorr_force}} |
| 792 |
> |
\end{figure} |
| 793 |
> |
|
| 794 |
> |
|
| 795 |
|
\begin{figure} |
| 796 |
< |
\centering |
| 797 |
< |
\includegraphics[width=0.5 \textwidth]{torquePlot_slopeCorrelation_combined-crop.pdf} |
| 798 |
< |
\caption{The correlation coefficient and regression slope of the magnitude of the torque for a given method with compared to the reference Ewald method. The value of result equal to 1(dashed line) indicates, the magnitude of the force from a method is indistinguishable from the Ewald method. Here different symbols represent different value of the cutoff radius (9 $A^o$ = circle, 12 $A^o$ = square 15 $A^o$ = inverted triangle).} |
| 799 |
< |
\label{fig:slopeCorr_torque} |
| 800 |
< |
\end{figure} |
| 796 |
> |
\centering |
| 797 |
> |
\includegraphics[width=0.6\linewidth]{torquePlot_slopeCorrelation_combined.eps} |
| 798 |
> |
\caption{Statistical analysis of the quality of the torque vector |
| 799 |
> |
magnitudes for the real-space electrostatic methods compared with |
| 800 |
> |
the reference Ewald sum. Results with a value equal to 1 (dashed |
| 801 |
> |
line) indicate force magnitude values indistinguishable from those |
| 802 |
> |
obtained using the multipolar Ewald sum. Different values of the |
| 803 |
> |
cutoff radius are indicated with different symbols (9~\AA\ = |
| 804 |
> |
circles, 12~\AA\ = squares, and 15~\AA\ = inverted |
| 805 |
> |
triangles).\label{fig:slopeCorr_torque}} |
| 806 |
> |
\end{figure} |
| 807 |
> |
|
| 808 |
> |
The torques (Fig. \ref{fig:slopeCorr_torque}) appear to be |
| 809 |
> |
significantly influenced by the choice of real-space method. The |
| 810 |
> |
torque expressions have the same distance dependence as the energies, |
| 811 |
> |
which are naturally longer-ranged expressions than the inter-site |
| 812 |
> |
forces. Torques are also quite sensitive to orientations of |
| 813 |
> |
neighboring molecules, even those that are near the cutoff distance. |
| 814 |
> |
|
| 815 |
> |
The results shows that the torque from the hard cutoff method |
| 816 |
> |
reproduces the torques in quite good agreement with the Ewald sum. |
| 817 |
> |
The other real-space methods can cause some deviations, but excellent |
| 818 |
> |
agreement with the Ewald sum torques is recovered at moderate values |
| 819 |
> |
of the damping coefficient ($\alpha \approx 0.2$~\AA$^{-1}$) and cutoff |
| 820 |
> |
radius ($r_c \ge 12$~\AA). The TSF method exhibits only fair agreement |
| 821 |
> |
in the slope when compared with the Ewald torques even for larger |
| 822 |
> |
cutoff radii. It appears that the severity of the perturbations in |
| 823 |
> |
the TSF method are most in evidence for the torques. |
| 824 |
> |
|
| 825 |
|
\subsection{Directionality of the force and torque vectors} |
| 674 |
– |
The accurate evaluation of the direction of the force and torques are also important for the dynamic simulation.In our research, the direction data sets were computed from the purposed method and compared with Ewald using Fisher statistics and results are expressed in terms of circular variance ($Var(\theta$).The force and torque vectors from the purposed method followed Fisher probability distribution function expressed in equation~\ref{eq:pdf}. The circular variance for the force and torque vectors of each molecule in the 250 configurations for all system types is shown in Figure~\ref{fig:slopeCorr_circularVariance}. The direction of the force and torque vectors from hard and SP cutoff methods showed best directional agreement with the Ewald. The force and torque vectors from GSF method also showed good agreement with the Ewald method, which can also be improved by varying damping alpha and cutoff radius.For $\alpha = 0.2$ and $r_c = 12 A^o$, $ Var(\theta) $ for direction of the force was found to be 0.002061 and corresponding value of $\kappa $ was 485.20. Integration of equation ~\ref{eq:pdf} for that corresponding value of $\kappa$ showed that 95\% of force vectors are with in $6.37^o$. The TSF method is the poorest in evaluating accurate direction with compared to Hard, SP, and GSF methods. The circular variance for the direction of the torques is larger as compared to force. For same $\alpha = 0.2, r_c = 12 A^o$ and GSF method, the circular variance was 0.01415, which showed 95\% of torque vectors are within $16.75^o$.The direction of the force and torque vectors can be improved by varying $\alpha$ and $r_c$. |
| 826 |
|
|
| 827 |
+ |
The accurate evaluation of force and torque directions is just as |
| 828 |
+ |
important for molecular dynamics simulations as the magnitudes of |
| 829 |
+ |
these quantities. Force and torque vectors for all six systems were |
| 830 |
+ |
analyzed using Fisher statistics, and the quality of the vector |
| 831 |
+ |
directionality is shown in terms of circular variance |
| 832 |
+ |
($\mathrm{Var}(\theta)$) in |
| 833 |
+ |
Fig. \ref{fig:slopeCorr_circularVariance}. The force and torque |
| 834 |
+ |
vectors from the new real-space methods exhibit nearly-ideal Fisher |
| 835 |
+ |
probability distributions (Eq.~\ref{eq:pdf}). Both the hard and SP |
| 836 |
+ |
cutoff methods exhibit the best vectorial agreement with the Ewald |
| 837 |
+ |
sum. The force and torque vectors from GSF method also show good |
| 838 |
+ |
agreement with the Ewald method, which can also be systematically |
| 839 |
+ |
improved by using moderate damping and a reasonable cutoff radius. For |
| 840 |
+ |
$\alpha = 0.2$~\AA$^{-1}$ and $r_c = 12$~\AA, we observe |
| 841 |
+ |
$\mathrm{Var}(\theta) = 0.00206$, which corresponds to a distribution |
| 842 |
+ |
with 95\% of force vectors within $6.37^\circ$ of the corresponding |
| 843 |
+ |
Ewald forces. The TSF method produces the poorest agreement with the |
| 844 |
+ |
Ewald force directions. |
| 845 |
+ |
|
| 846 |
+ |
Torques are again more perturbed than the forces by the new real-space |
| 847 |
+ |
methods, but even here the variance is reasonably small. For the same |
| 848 |
+ |
method (GSF) with the same parameters ($\alpha = 0.2$~\AA$^{-1}$, $r_c |
| 849 |
+ |
= 12$~\AA), the circular variance was 0.01415, corresponds to a |
| 850 |
+ |
distribution which has 95\% of torque vectors are within $16.75^\circ$ |
| 851 |
+ |
of the Ewald results. Again, the direction of the force and torque |
| 852 |
+ |
vectors can be systematically improved by varying $\alpha$ and $r_c$. |
| 853 |
+ |
|
| 854 |
|
\begin{figure} |
| 855 |
< |
\centering |
| 856 |
< |
\includegraphics[width=0.5 \textwidth]{Variance_forceNtorque_modified-crop.pdf} |
| 857 |
< |
\caption{The circular variance of the data sets of the |
| 858 |
< |
direction of the force and torque vectors obtained from a |
| 859 |
< |
given method about reference Ewald method. The result equal |
| 860 |
< |
to 0 (dashed line) indicates direction of the vectors are |
| 861 |
< |
indistinguishable from the Ewald method. Here different |
| 862 |
< |
symbols represent different value of the cutoff radius (9 |
| 863 |
< |
\AA\ = circle, 12 \AA\ = square, 15 \AA\ = inverted triangle)} |
| 864 |
< |
\label{fig:slopeCorr_circularVariance} |
| 687 |
< |
\end{figure} |
| 688 |
< |
\subsection{Total energy conservation} |
| 689 |
< |
We have tested the conservation of energy in the SSDQC liquid system |
| 690 |
< |
by running system for 1ns in the Hard, SP, GSF and TSF method. The |
| 691 |
< |
Hard cutoff method shows very high energy drifts 433.53 |
| 692 |
< |
KCal/Mol/ns/particle and energy fluctuation 32574.53 Kcal/Mol |
| 693 |
< |
(measured by the SD from the slope) for the undamped case, which makes |
| 694 |
< |
it completely unusable in MD simulations. The SP method also shows |
| 695 |
< |
large value of energy drift 1.289 Kcal/Mol/ns/particle and energy |
| 696 |
< |
fluctuation 0.01953 Kcal/Mol. The energy fluctuation in the SP method |
| 697 |
< |
is due to the non-vanishing nature of the torque and force at the |
| 698 |
< |
cutoff radius. We can improve the energy conservation in some extent |
| 699 |
< |
by the proper selection of the damping alpha but the improvement is |
| 700 |
< |
not good enough, which can be observed in Figure 9a and 9b .The GSF |
| 701 |
< |
and TSF shows very low value of energy drift 0.09016, 0.07371 |
| 702 |
< |
KCal/Mol/ns/particle and fluctuation 3.016E-6, 1.217E-6 Kcal/Mol |
| 703 |
< |
respectively for the undamped case. Since the absolute value of the |
| 704 |
< |
evaluated electrostatic energy, force and torque from TSF method are |
| 705 |
< |
deviated from the Ewald, it does not mimic MD simulations |
| 706 |
< |
appropriately. The electrostatic energy, force and torque from the GSF |
| 707 |
< |
method have very good agreement with the Ewald. In addition, the |
| 708 |
< |
energy drift and energy fluctuation from the GSF method is much better |
| 709 |
< |
than Ewald’s method for reciprocal space vector value ($k_f$) equal to |
| 710 |
< |
7 as shown in Figure~\ref{fig:energyDrift} and |
| 711 |
< |
~\ref{fig:fluctuation}. We can improve the total energy fluctuation |
| 712 |
< |
and drift for the Ewald’s method by increasing size of the reciprocal |
| 713 |
< |
space, which extremely increseses the simulation time. In our current |
| 714 |
< |
simulation, the simulation time for the Hard, SP, and GSF methods are |
| 715 |
< |
about 5.5 times faster than the Ewald method. |
| 855 |
> |
\centering |
| 856 |
> |
\includegraphics[width=0.65\linewidth]{Variance_forceNtorque_modified.eps} |
| 857 |
> |
\caption{The circular variance of the direction of the force and |
| 858 |
> |
torque vectors obtained from the real-space methods around the |
| 859 |
> |
reference Ewald vectors. A variance equal to 0 (dashed line) |
| 860 |
> |
indicates direction of the force or torque vectors are |
| 861 |
> |
indistinguishable from those obtained from the Ewald sum. Here |
| 862 |
> |
different symbols represent different values of the cutoff radius |
| 863 |
> |
(9~\AA\ = circle, 12~\AA\ = square, 15~\AA\ = inverted triangle)\label{fig:slopeCorr_circularVariance}} |
| 864 |
> |
\end{figure} |
| 865 |
|
|
| 866 |
< |
In Fig.~\ref{fig:energyDrift}, $\delta \mbox{E}_1$ is a measure of the |
| 718 |
< |
linear energy drift in units of $\mbox{kcal mol}^{-1}$ per particle |
| 719 |
< |
over a nanosecond of simulation time, and $\delta \mbox{E}_0$ is the |
| 720 |
< |
standard deviation of the energy fluctuations in units of $\mbox{kcal |
| 721 |
< |
mol}^{-1}$ per particle. In the bottom plot, it is apparent that the |
| 722 |
< |
energy drift is reduced by a significant amount (2 to 3 orders of |
| 723 |
< |
magnitude improvement at all values of the damping coefficient) by |
| 724 |
< |
chosing either of the shifted-force methods over the hard or SP |
| 725 |
< |
methods. We note that the two shifted-force method can give |
| 726 |
< |
significantly better energy conservation than the multipolar Ewald sum |
| 727 |
< |
with the same choice of real-space cutoffs. |
| 866 |
> |
\subsection{Energy conservation\label{sec:conservation}} |
| 867 |
|
|
| 868 |
+ |
We have tested the conservation of energy one can expect to see with |
| 869 |
+ |
the new real-space methods using the soft DQ liquid model with a small |
| 870 |
+ |
fraction of solvated ions. This is a test system which exercises all |
| 871 |
+ |
orders of multipole-multipole interactions derived in the first paper |
| 872 |
+ |
in this series and provides the most comprehensive test of the new |
| 873 |
+ |
methods. A liquid-phase system was created with 2000 liquid-phase |
| 874 |
+ |
molecules and 48 dissolved ions at a density of 0.98 g cm$^{-3}$ and a |
| 875 |
+ |
temperature of 300K. After equilibration in the canonical (NVT) |
| 876 |
+ |
ensemble using a Nos\'e-Hoover thermostat, this liquid-phase system |
| 877 |
+ |
was run for 1 ns in the microcanonical (NVE) ensemble under the Ewald, |
| 878 |
+ |
Hard, SP, GSF, and TSF methods with a cutoff radius of 12~\AA. The |
| 879 |
+ |
value of the damping coefficient was also varied from the undamped |
| 880 |
+ |
case ($\alpha = 0$) to a heavily damped case ($\alpha = |
| 881 |
+ |
0.3$~\AA$^{-1}$) for all of the real space methods. A sample was also |
| 882 |
+ |
run using the multipolar Ewald sum with the same real-space cutoff. |
| 883 |
+ |
|
| 884 |
+ |
In figure~\ref{fig:energyDrift} we show the both the linear drift in |
| 885 |
+ |
energy over time, $\delta E_1$, and the standard deviation of energy |
| 886 |
+ |
fluctuations around this drift $\delta E_0$. Both of the |
| 887 |
+ |
shifted-force methods (GSF and TSF) provide excellent energy |
| 888 |
+ |
conservation (drift less than $10^{-5}$ kcal / mol / ns / particle), |
| 889 |
+ |
while the hard cutoff is essentially unusable for molecular dynamics. |
| 890 |
+ |
SP provides some benefit over the hard cutoff because the energetic |
| 891 |
+ |
jumps that happen as particles leave and enter the cutoff sphere are |
| 892 |
+ |
somewhat reduced, but like the Wolf method for charges, the SP method |
| 893 |
+ |
would not be as useful for molecular dynamics as either of the |
| 894 |
+ |
shifted-force methods. |
| 895 |
+ |
|
| 896 |
+ |
We note that for all tested values of the cutoff radius, the new |
| 897 |
+ |
real-space methods can provide better energy conservation behavior |
| 898 |
+ |
than the multipolar Ewald sum, even when relatively large $k$-space |
| 899 |
+ |
cutoff values are utilized. |
| 900 |
+ |
|
| 901 |
|
\begin{figure} |
| 902 |
|
\centering |
| 903 |
< |
\includegraphics[width=\textwidth]{newDrift.pdf} |
| 904 |
< |
\label{fig:energyDrift} |
| 905 |
< |
\caption{Analysis of the energy conservation of the real space |
| 906 |
< |
electrostatic methods. $\delta \mathrm{E}_1$ is the linear drift in |
| 907 |
< |
energy over time and $\delta \mathrm{E}_0$ is the standard deviation |
| 908 |
< |
of energy fluctuations around this drift. All simulations were of a |
| 909 |
< |
2000-molecule simulation of SSDQ water with 48 ionic charges at 300 |
| 910 |
< |
K starting from the same initial configuration.} |
| 903 |
> |
\includegraphics[width=\textwidth]{newDrift_12.eps} |
| 904 |
> |
\caption{Energy conservation of the real-space methods for the soft |
| 905 |
> |
DQ liauid / ion system. $\delta \mathrm{E}_1$ is the linear drift |
| 906 |
> |
in energy over time (in kcal/mol/particle/ns) and $\delta |
| 907 |
> |
\mathrm{E}_0$ is the standard deviation of energy fluctuations |
| 908 |
> |
around this drift (in kcal/mol/particle). Points that appear in |
| 909 |
> |
the green region at the bottom exhibit better energy conservation |
| 910 |
> |
than would be obtained using common parameters for Ewald-based |
| 911 |
> |
electrostatics.\label{fig:energyDrift}} |
| 912 |
|
\end{figure} |
| 913 |
|
|
| 914 |
+ |
\subsection{Reproduction of Structural \& Dynamical Features\label{sec:structure}} |
| 915 |
+ |
The most important test of the modified interaction potentials is the |
| 916 |
+ |
fidelity with which they can reproduce structural features and |
| 917 |
+ |
dynamical properties in a liquid. One commonly-utilized measure of |
| 918 |
+ |
structural ordering is the pair distribution function, $g(r)$, which |
| 919 |
+ |
measures local density deviations in relation to the bulk density. In |
| 920 |
+ |
the electrostatic approaches studied here, the short-range repulsion |
| 921 |
+ |
from the Lennard-Jones potential is identical for the various |
| 922 |
+ |
electrostatic methods, and since short range repulsion determines much |
| 923 |
+ |
of the local liquid ordering, one would not expect to see many |
| 924 |
+ |
differences in $g(r)$. Indeed, the pair distributions are essentially |
| 925 |
+ |
identical for all of the electrostatic methods studied (for each of |
| 926 |
+ |
the different systems under investigation). |
| 927 |
+ |
|
| 928 |
+ |
% An example of this agreement for the soft DQ liquid/ion system is |
| 929 |
+ |
% shown in Fig. \ref{fig:gofr}. |
| 930 |
+ |
|
| 931 |
+ |
% \begin{figure} |
| 932 |
+ |
% \centering |
| 933 |
+ |
% \includegraphics[width=\textwidth]{gofr_ssdqc.eps} |
| 934 |
+ |
% \caption{The pair distribution functions, $g(r)$, for the SSDQ |
| 935 |
+ |
% water/ion system obtained using the different real-space methods are |
| 936 |
+ |
% essentially identical with the result from the Ewald |
| 937 |
+ |
% treatment.\label{fig:gofr}} |
| 938 |
+ |
% \end{figure} |
| 939 |
+ |
|
| 940 |
+ |
There is a minor over-structuring of the first solvation shell when |
| 941 |
+ |
using TSF or when overdamping with any of the real-space methods. |
| 942 |
+ |
With moderate damping, GSF and SP produce pair distributions that are |
| 943 |
+ |
identical (within numerical noise) to their Ewald counterparts. The |
| 944 |
+ |
degree of over-structuring can be measured most easily using the |
| 945 |
+ |
coordination number, |
| 946 |
+ |
\begin{equation} |
| 947 |
+ |
n_C = 4\pi\rho \int_{0}^{a}r^2\text{g}(r)dr, |
| 948 |
+ |
\end{equation} |
| 949 |
+ |
where $\rho$ is the number density of the site-site pair interactions, |
| 950 |
+ |
and $a$ is the radial location of the minima following the first peak |
| 951 |
+ |
in $g(r)$ ($a = 4.2$~\AA\ for the soft DQ liquid / ion system). The |
| 952 |
+ |
coordination number is shown as a function of the damping coefficient |
| 953 |
+ |
for all of the real space methods in Fig. \ref{fig:Props}. |
| 954 |
+ |
|
| 955 |
+ |
A more demanding test of modified electrostatics is the average value |
| 956 |
+ |
of the electrostatic energy $\langle U_\mathrm{elect} \rangle / N$ |
| 957 |
+ |
which is obtained by sampling the liquid-state configurations |
| 958 |
+ |
experienced by a liquid evolving entirely under the influence of each |
| 959 |
+ |
of the methods. In Fig. \ref{fig:Props} we demonstrate how $\langle |
| 960 |
+ |
U_\mathrm{elect} \rangle / N$ varies with the damping parameter, |
| 961 |
+ |
$\alpha$, for each of the methods. |
| 962 |
+ |
|
| 963 |
+ |
As in the crystals studied in the first paper, damping is important |
| 964 |
+ |
for converging the mean electrostatic energy values, particularly for |
| 965 |
+ |
the two shifted force methods (GSF and TSF). A value of $\alpha |
| 966 |
+ |
\approx 0.2$~\AA$^{-1}$ is sufficient to converge the SP and GSF |
| 967 |
+ |
energies with a cutoff of 12 \AA, while shorter cutoffs require more |
| 968 |
+ |
dramatic damping ($\alpha \approx 0.28$~\AA$^{-1}$ for $r_c = 9$~\AA). |
| 969 |
+ |
Overdamping the real-space electrostatic methods occurs with $\alpha > |
| 970 |
+ |
0.3$~\AA$^{-1}$, causing the estimate of the electrostatic energy to |
| 971 |
+ |
drop below the Ewald results. |
| 972 |
+ |
|
| 973 |
+ |
These ``optimal'' values of the damping coefficient for structural |
| 974 |
+ |
features are similar to those observed for DSF electrostatics for |
| 975 |
+ |
purely point-charge systems, and the range $\alpha= 0.175 \rightarrow |
| 976 |
+ |
0.225$~\AA$^{-1}$ for $r_c = 12$~\AA\ appears to be an excellent |
| 977 |
+ |
compromise for mixed charge/multipolar systems. |
| 978 |
+ |
|
| 979 |
+ |
To test the fidelity of the electrostatic methods at reproducing |
| 980 |
+ |
\textit{dynamics} in a multipolar liquid, it is also useful to look at |
| 981 |
+ |
transport properties, particularly the diffusion constant, |
| 982 |
+ |
\begin{equation} |
| 983 |
+ |
D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle \left| |
| 984 |
+ |
\mathbf{r}(t) -\mathbf{r}(0) \right|^2 \rangle |
| 985 |
+ |
\label{eq:diff} |
| 986 |
+ |
\end{equation} |
| 987 |
+ |
which measures long-time behavior and is sensitive to the forces on |
| 988 |
+ |
the multipoles. The self-diffusion constants (D) were calculated from |
| 989 |
+ |
linear fits to the long-time portion of the mean square displacement, |
| 990 |
+ |
$\langle r^{2}(t) \rangle$.\cite{Allen87} In Fig. \ref{fig:Props} we |
| 991 |
+ |
demonstrate how the diffusion constant depends on the choice of |
| 992 |
+ |
real-space methods and the damping coefficient. Both the SP and GSF |
| 993 |
+ |
methods can obtain excellent agreement with Ewald again using moderate |
| 994 |
+ |
damping. |
| 995 |
+ |
|
| 996 |
+ |
In addition to translational diffusion, orientational relaxation times |
| 997 |
+ |
were calculated for comparisons with the Ewald simulations and with |
| 998 |
+ |
experiments. These values were determined by calculating the |
| 999 |
+ |
orientational time correlation function, |
| 1000 |
+ |
\begin{equation} |
| 1001 |
+ |
C_l^\gamma(t) = \left\langle P_l\left[\hat{\mathbf{A}}_\gamma(t) |
| 1002 |
+ |
\cdot\hat{\mathbf{A}}_\gamma(0)\right]\right\rangle, |
| 1003 |
+ |
\label{eq:OrientCorr} |
| 1004 |
+ |
\end{equation} |
| 1005 |
+ |
from the same 350 ps microcanonical trajectories that were used for |
| 1006 |
+ |
translational diffusion. Here, $P_l$ is the Legendre polynomial of |
| 1007 |
+ |
order $l$ and $\hat{\mathbf{A}}_\gamma$ is the unit vector for body |
| 1008 |
+ |
axis $\gamma$. The reference frame used for our sample dipolar |
| 1009 |
+ |
systems has the $z$-axis running along the dipoles, and for the soft |
| 1010 |
+ |
DQ liquid model, the $y$-axis connects the two implied hydrogen-like |
| 1011 |
+ |
positions. From the orientation autocorrelation functions, we can |
| 1012 |
+ |
obtain time constants for rotational relaxation either by fitting to a |
| 1013 |
+ |
multi-exponential model for the orientational relaxation, or by |
| 1014 |
+ |
integrating the correlation functions. |
| 1015 |
+ |
|
| 1016 |
+ |
In a good model for water, the orientational decay times would be |
| 1017 |
+ |
comparable to water orientational relaxation times from nuclear |
| 1018 |
+ |
magnetic resonance (NMR). The relaxation constant obtained from |
| 1019 |
+ |
$C_2^y(t)$ is normally of experimental interest because it describes |
| 1020 |
+ |
the relaxation of the principle axis connecting the hydrogen |
| 1021 |
+ |
atoms. Thus, $C_2^y(t)$ can be compared to the intermolecular portion |
| 1022 |
+ |
of the dipole-dipole relaxation from a proton NMR signal and can |
| 1023 |
+ |
provide an estimate of the NMR relaxation time constant.\cite{Impey82} |
| 1024 |
+ |
In Fig. \ref{fig:Props} we compare the $\tau_2^y$ and $\tau_2^z$ |
| 1025 |
+ |
values for the various real-space methods over a range of different |
| 1026 |
+ |
damping coefficients. The rotational relaxation for the $z$ axis |
| 1027 |
+ |
primarily probes the torques on the dipoles, while the relaxation for |
| 1028 |
+ |
the $y$ axis is sensitive primarily to the quadrupolar torques. |
| 1029 |
+ |
|
| 1030 |
+ |
\begin{figure} |
| 1031 |
+ |
\includegraphics[width=\textwidth]{properties.eps} |
| 1032 |
+ |
\caption{Comparison of the structural and dynamic properties for the |
| 1033 |
+ |
combined multipolar liquid (soft DQ liquid + ions) for all of the |
| 1034 |
+ |
real-space methods with $r_c = 12$~\AA. Electrostatic energies, |
| 1035 |
+ |
$\langle U_\mathrm{elect} \rangle / N$ (in kcal / mol), |
| 1036 |
+ |
coordination numbers, $n_C$, diffusion constants (in $10^{-5} |
| 1037 |
+ |
\mathrm{cm}^2\mathrm{s}^{-1}$), and rotational correlation times |
| 1038 |
+ |
(in ps) all show excellent agreement with Ewald results for |
| 1039 |
+ |
damping coefficients in the range $\alpha= 0.175 \rightarrow |
| 1040 |
+ |
0.225$~\AA$^{-1}$. \label{fig:Props}} |
| 1041 |
+ |
\end{figure} |
| 1042 |
+ |
|
| 1043 |
+ |
In Fig. \ref{fig:Props} it appears that values for $D$, $\tau_2^y$, |
| 1044 |
+ |
and $\tau_2^z$ using the Ewald sum are reproduced with excellent |
| 1045 |
+ |
fidelity by the GSF and SP methods. All of the real space methods can |
| 1046 |
+ |
be \textit{overdamped}, which reduces the effective range of multipole |
| 1047 |
+ |
interactions, causing structural and dynamical changes from the |
| 1048 |
+ |
correct behavior. Because overdamping weakens orientational |
| 1049 |
+ |
preferences between adjacent molecules, it manifests as too-rapid |
| 1050 |
+ |
orientational decay coupled with faster diffusion and |
| 1051 |
+ |
over-coordination of the liquid. Underdamping is less problematic for |
| 1052 |
+ |
the SP and GSF methods, as their structural and dynamical properties |
| 1053 |
+ |
still reproduce the Ewald results even in the completely undamped |
| 1054 |
+ |
($\alpha = 0$) case. An optimal range for the electrostatic damping |
| 1055 |
+ |
parameter appears to be $\alpha= 0.175 \rightarrow 0.225$~\AA$^{-1}$ |
| 1056 |
+ |
for $r_c = 12$~\AA, which similar to the optimal range found for the |
| 1057 |
+ |
damped shifted force potential for point charges.\cite{Fennell:2006lq} |
| 1058 |
+ |
|
| 1059 |
|
\section{CONCLUSION} |
| 1060 |
< |
We have generalized the charged neutralized potential energy originally developed by the Wolf et al.\cite{Wolf:1999dn} for the charge-charge interaction to the charge-multipole and multipole-multipole interaction in the SP method for higher order multipoles. Also, we have developed GSF and TSF methods by implementing the modification purposed by Fennel and Gezelter\cite{Fennell:2006lq} for the charge-charge interaction to the higher order multipoles to ensure consistency and smooth truncation of the electrostatic energy, force, and torque for the spherical truncation. The SP methods for multipoles proved its suitability in MC simulations. On the other hand, the results from the GSF method produced good agreement with the Ewald's energy, force, and torque. Also, it shows very good energy conservation in MD simulations. |
| 1061 |
< |
The direct truncation of any molecular system without multipole neutralization creates the fluctuation in the electrostatic energy. This fluctuation in the energy is very large for the case of crystal because of long range of multipole ordering (Refer paper I).\cite{PaperI} This is also significant in the case of the liquid because of the local multipole ordering in the molecules. If the net multipole within cutoff radius neutralized within cutoff sphere by placing image multiples on the surface of the sphere, this fluctuation in the energy reduced significantly. Also, the multipole neutralization in the generalized SP method showed very good agreement with the Ewald as compared to direct truncation for the evaluation of the $\triangle E$ between the configurations. |
| 1062 |
< |
In MD simulations, the energy conservation is very important. The |
| 1063 |
< |
conservation of the total energy can be ensured by i) enforcing the |
| 1064 |
< |
smooth truncation of the energy, force and torque in the cutoff radius |
| 1065 |
< |
and ii) making the energy, force and torque consistent with each |
| 1066 |
< |
other. The GSF and TSF methods ensure the consistency and smooth |
| 1067 |
< |
truncation of the energy, force and torque at the cutoff radius, as a |
| 1068 |
< |
result show very good total energy conservation. But the TSF method |
| 751 |
< |
does not show good agreement in the absolute value of the |
| 752 |
< |
electrostatic energy, force and torque with the Ewald. The GSF method |
| 753 |
< |
has mimicked Ewald’s force, energy and torque accurately and also |
| 754 |
< |
conserved energy. Therefore, the GSF method is the suitable method for |
| 755 |
< |
evaluating required force field in MD simulations. In addition, the |
| 756 |
< |
energy drift and fluctuation from the GSF method is much better than |
| 757 |
< |
Ewald’s method for finite-sized reciprocal space. |
| 1060 |
> |
In the first paper in this series, we generalized the |
| 1061 |
> |
charge-neutralized electrostatic energy originally developed by Wolf |
| 1062 |
> |
\textit{et al.}\cite{Wolf:1999dn} to multipole-multipole interactions |
| 1063 |
> |
up to quadrupolar order. The SP method is essentially a |
| 1064 |
> |
multipole-capable version of the Wolf model. The SP method for |
| 1065 |
> |
multipoles provides excellent agreement with Ewald-derived energies, |
| 1066 |
> |
forces and torques, and is suitable for Monte Carlo simulations, |
| 1067 |
> |
although the forces and torques retain discontinuities at the cutoff |
| 1068 |
> |
distance that prevents its use in molecular dynamics. |
| 1069 |
|
|
| 1070 |
< |
Note that the TSF, GSF, and SP models are $\mathcal{O}(N)$ methods |
| 1071 |
< |
that can be made extremely efficient using spline interpolations of |
| 1072 |
< |
the radial functions. They require no Fourier transforms or $k$-space |
| 1073 |
< |
sums, and guarantee the smooth handling of energies, forces, and |
| 1074 |
< |
torques as multipoles cross the real-space cutoff boundary. |
| 1070 |
> |
We also developed two natural extensions of the damped shifted-force |
| 1071 |
> |
(DSF) model originally proposed by Zahn {\it et al.} and extended by |
| 1072 |
> |
Fennell and Gezelter.\cite{Zahn:2002hc,Fennell:2006lq} The GSF and TSF |
| 1073 |
> |
approaches provide smooth truncation of energies, forces, and torques |
| 1074 |
> |
at the real-space cutoff, and both converge to DSF electrostatics for |
| 1075 |
> |
point-charge interactions. The TSF model is based on a high-order |
| 1076 |
> |
truncated Taylor expansion which can be relatively perturbative inside |
| 1077 |
> |
the cutoff sphere. The GSF model takes the gradient from an images of |
| 1078 |
> |
the interacting multipole that has been projected onto the cutoff |
| 1079 |
> |
sphere to derive shifted force and torque expressions, and is a |
| 1080 |
> |
significantly more gentle approach. |
| 1081 |
|
|
| 1082 |
+ |
The GSF method produces quantitative agreement with Ewald energies, |
| 1083 |
+ |
forces, and torques. It also performs well in conserving energy in MD |
| 1084 |
+ |
simulations. The Taylor-shifted (TSF) model provides smooth dynamics, |
| 1085 |
+ |
but these take place on a potential energy surface that is |
| 1086 |
+ |
significantly perturbed from Ewald-based electrostatics. Because it |
| 1087 |
+ |
performs relatively poorly compared with GSF, it may seem odd that |
| 1088 |
+ |
that the TSF model was included in this work. However, the functional |
| 1089 |
+ |
forms derived for the SP and GSF methods depend on the separation of |
| 1090 |
+ |
orientational contributions that were made visible by the Taylor |
| 1091 |
+ |
series of the electrostatic kernel at the cutoff radius. The TSF |
| 1092 |
+ |
method also has the unique property that a large number of derivatives |
| 1093 |
+ |
can be made to vanish at the cutoff radius. This property has proven |
| 1094 |
+ |
useful in past treatments of the corrections to the Clausius-Mossotti |
| 1095 |
+ |
fluctuation formula for dielectric constants.\cite{Izvekov:2008wo} |
| 1096 |
+ |
|
| 1097 |
+ |
Reproduction of both structural and dynamical features in the liquid |
| 1098 |
+ |
systems is remarkably good for both the SP and GSF models. Pair |
| 1099 |
+ |
distribution functions are essentially equivalent to the same |
| 1100 |
+ |
functions produced using Ewald-based electrostatics, and with moderate |
| 1101 |
+ |
damping, a structural feature that directly probes the electrostatic |
| 1102 |
+ |
interaction (e.g. the mean electrostatic potential energy) can also be |
| 1103 |
+ |
made quantitative. Dynamical features are sensitive probes of the |
| 1104 |
+ |
forces and torques produced by these methods, and even though the |
| 1105 |
+ |
smooth behavior of forces is produced by perturbing the overall |
| 1106 |
+ |
potential, the diffusion constants and orientational correlation times |
| 1107 |
+ |
are quite close to the Ewald-based results. |
| 1108 |
+ |
|
| 1109 |
+ |
The only cases we have found where the new GSF and SP real-space |
| 1110 |
+ |
methods can be problematic are those which retain a bulk dipole moment |
| 1111 |
+ |
at large distances (e.g. the $Z_1$ dipolar lattice). In ferroelectric |
| 1112 |
+ |
materials, uniform weighting of the orientational contributions can be |
| 1113 |
+ |
important for converging the total energy. In these cases, the |
| 1114 |
+ |
damping function which causes the non-uniform weighting can be |
| 1115 |
+ |
replaced by the bare electrostatic kernel, and the energies return to |
| 1116 |
+ |
the expected converged values. |
| 1117 |
+ |
|
| 1118 |
+ |
Based on the results of this work, we can conclude that the GSF method |
| 1119 |
+ |
is a suitable and efficient replacement for the Ewald sum for |
| 1120 |
+ |
evaluating electrostatic interactions in modern MD simulations, and |
| 1121 |
+ |
the SP method would be an excellent choice for Monte Carlo |
| 1122 |
+ |
simulations where smooth forces and energy conservation are not |
| 1123 |
+ |
important. Both the SP and GSF methods retain excellent fidelity to |
| 1124 |
+ |
the Ewald energies, forces and torques. Additionally, the energy |
| 1125 |
+ |
drift and fluctuations from the GSF electrostatics are significantly |
| 1126 |
+ |
better than a multipolar Ewald sum for finite-sized reciprocal spaces, |
| 1127 |
+ |
and physical properties are reproduced accurately. |
| 1128 |
+ |
|
| 1129 |
+ |
As in all purely pairwise cutoff methods, the SP, GSF and TSF methods |
| 1130 |
+ |
are expected to scale approximately {\it linearly} with system size, |
| 1131 |
+ |
and are easily parallelizable. This should result in substantial |
| 1132 |
+ |
reductions in the computational cost of performing large simulations. |
| 1133 |
+ |
With the proper use of pre-computation and spline interpolation of the |
| 1134 |
+ |
radial functions, the real-space methods are essentially the same cost |
| 1135 |
+ |
as a simple real-space cutoff. They require no Fourier transforms or |
| 1136 |
+ |
$k$-space sums, and guarantee the smooth handling of energies, forces, |
| 1137 |
+ |
and torques as multipoles cross the real-space cutoff boundary. |
| 1138 |
+ |
|
| 1139 |
+ |
We are not suggesting that there is any flaw with the Ewald sum; in |
| 1140 |
+ |
fact, it is the standard by which the SP, GSF, and TSF methods have |
| 1141 |
+ |
been judged in this work. However, these results provide evidence |
| 1142 |
+ |
that in the typical simulations performed today, the Ewald summation |
| 1143 |
+ |
may no longer be required to obtain the level of accuracy most |
| 1144 |
+ |
researchers have come to expect. |
| 1145 |
+ |
|
| 1146 |
+ |
\begin{acknowledgments} |
| 1147 |
+ |
JDG acknowledges helpful discussions with Christopher |
| 1148 |
+ |
Fennell. Support for this project was provided by the National |
| 1149 |
+ |
Science Foundation under grant CHE-1362211. Computational time was |
| 1150 |
+ |
provided by the Center for Research Computing (CRC) at the |
| 1151 |
+ |
University of Notre Dame. |
| 1152 |
+ |
\end{acknowledgments} |
| 1153 |
+ |
|
| 1154 |
|
%\bibliographystyle{aip} |
| 1155 |
|
\newpage |
| 1156 |
|
\bibliography{references} |
