16 |
|
|
17 |
|
Integration schemes for rotational motion of the rigid molecules in |
18 |
|
microcanonical ensemble have been extensively studied in the last |
19 |
< |
two decades. Matubayasi and Nakahara developed a time-reversible |
20 |
< |
integrator for rigid bodies in quaternion representation. Although |
21 |
< |
it is not symplectic, this integrator still demonstrates a better |
22 |
< |
long-time energy conservation than traditional methods because of |
23 |
< |
the time-reversible nature. Extending Trotter-Suzuki to general |
24 |
< |
system with a flat phase space, Miller and his colleagues devised an |
25 |
< |
novel symplectic, time-reversible and volume-preserving integrator |
26 |
< |
in quaternion representation, which was shown to be superior to the |
27 |
< |
time-reversible integrator of Matubayasi and Nakahara. However, all |
28 |
< |
of the integrators in quaternion representation suffer from the |
19 |
> |
two decades. Matubayasi developed a time-reversible integrator for |
20 |
> |
rigid bodies in quaternion representation. Although it is not |
21 |
> |
symplectic, this integrator still demonstrates a better long-time |
22 |
> |
energy conservation than traditional methods because of the |
23 |
> |
time-reversible nature. Extending Trotter-Suzuki to general system |
24 |
> |
with a flat phase space, Miller and his colleagues devised an novel |
25 |
> |
symplectic, time-reversible and volume-preserving integrator in |
26 |
> |
quaternion representation, which was shown to be superior to the |
27 |
> |
Matubayasi's time-reversible integrator. However, all of the |
28 |
> |
integrators in quaternion representation suffer from the |
29 |
|
computational penalty of constructing a rotation matrix from |
30 |
|
quaternions to evolve coordinates and velocities at every time step. |
31 |
|
An alternative integration scheme utilizing rotation matrix directly |
139 |
|
average 7\% increase in computation time using the DLM method in |
140 |
|
place of quaternions. This cost is more than justified when |
141 |
|
comparing the energy conservation of the two methods as illustrated |
142 |
< |
in Fig.~\ref{timestep}. |
142 |
> |
in Fig.~\ref{methodFig:timestep}. |
143 |
|
|
144 |
|
\begin{figure} |
145 |
|
\centering |
474 |
|
\end{equation} |
475 |
|
|
476 |
|
Bond constraints are applied at the end of both the {\tt moveA} and |
477 |
< |
{\tt moveB} portions of the algorithm. Details on the constraint |
478 |
< |
algorithms are given in section \ref{oopseSec:rattle}. |
477 |
> |
{\tt moveB} portions of the algorithm. |
478 |
|
|
479 |
|
\subsection{\label{methodSection:NPTf}Constant-pressure integration with a |
480 |
|
flexible box (NPTf)} |
607 |
|
|
608 |
|
\subsection{\label{methodSection:otherSpecialEnsembles}Other Special Ensembles} |
609 |
|
|
610 |
< |
\subsubsection{\label{methodSection:NPAT}NPAT Ensemble} |
610 |
> |
\subsubsection{\label{methodSection:NPAT}\textbf{NPAT Ensemble}} |
611 |
|
|
612 |
|
A comprehensive understanding of structure¨Cfunction relations of |
613 |
|
biological membrane system ultimately relies on structure and |
630 |
|
Note that the iterative schemes for NPAT are identical to those |
631 |
|
described for the NPTi integrator. |
632 |
|
|
633 |
< |
\subsubsection{\label{methodSection:NPrT}NP$\gamma$T Ensemble} |
633 |
> |
\subsubsection{\label{methodSection:NPrT}\textbf{NP$\gamma$T Ensemble}} |
634 |
|
|
635 |
|
Theoretically, the surface tension $\gamma$ of a stress free |
636 |
|
membrane system should be zero since its surface free energy $G$ is |
668 |
|
integrator is a special case of $NP\gamma T$ if the surface tension |
669 |
|
$\gamma$ is set to zero. |
670 |
|
|
671 |
< |
%\section{\label{methodSection:constraintMethod}Constraint Method} |
671 |
> |
\section{\label{methodSection:zcons}Z-Constraint Method} |
672 |
|
|
673 |
< |
%\subsection{\label{methodSection:bondConstraint}Bond Constraint for Rigid Body} |
673 |
> |
Based on the fluctuation-dissipation theorem, a force |
674 |
> |
auto-correlation method was developed by Roux and Karplus to |
675 |
> |
investigate the dynamics of ions inside ion channels\cite{Roux1991}. |
676 |
> |
The time-dependent friction coefficient can be calculated from the |
677 |
> |
deviation of the instantaneous force from its mean force. |
678 |
> |
\begin{equation} |
679 |
> |
\xi(z,t)=\langle\delta F(z,t)\delta F(z,0)\rangle/k_{B}T, |
680 |
> |
\end{equation} |
681 |
> |
where% |
682 |
> |
\begin{equation} |
683 |
> |
\delta F(z,t)=F(z,t)-\langle F(z,t)\rangle. |
684 |
> |
\end{equation} |
685 |
|
|
686 |
< |
%\subsection{\label{methodSection:zcons}Z-constraint Method} |
686 |
> |
If the time-dependent friction decays rapidly, the static friction |
687 |
> |
coefficient can be approximated by |
688 |
> |
\begin{equation} |
689 |
> |
\xi_{\text{static}}(z)=\int_{0}^{\infty}\langle\delta F(z,t)\delta |
690 |
> |
F(z,0)\rangle dt. |
691 |
> |
\end{equation} |
692 |
> |
Allowing diffusion constant to then be calculated through the |
693 |
> |
Einstein relation:\cite{Marrink1994} |
694 |
> |
\begin{equation} |
695 |
> |
D(z)=\frac{k_{B}T}{\xi_{\text{static}}(z)}=\frac{(k_{B}T)^{2}}{\int_{0}^{\infty |
696 |
> |
}\langle\delta F(z,t)\delta F(z,0)\rangle dt}.% |
697 |
> |
\end{equation} |
698 |
|
|
699 |
< |
\section{\label{methodSection:langevin}Integrators for Langevin Dynamics of Rigid Bodies} |
700 |
< |
|
701 |
< |
\subsection{\label{methodSection:temperature}Temperature Control} |
702 |
< |
|
703 |
< |
\subsection{\label{methodSection:pressureControl}Pressure Control} |
704 |
< |
|
705 |
< |
\section{\label{methodSection:hydrodynamics}Hydrodynamics} |
699 |
> |
The Z-Constraint method, which fixes the z coordinates of the |
700 |
> |
molecules with respect to the center of the mass of the system, has |
701 |
> |
been a method suggested to obtain the forces required for the force |
702 |
> |
auto-correlation calculation.\cite{Marrink1994} However, simply |
703 |
> |
resetting the coordinate will move the center of the mass of the |
704 |
> |
whole system. To avoid this problem, we reset the forces of |
705 |
> |
z-constrained molecules as well as subtract the total constraint |
706 |
> |
forces from the rest of the system after the force calculation at |
707 |
> |
each time step instead of resetting the coordinate. |
708 |
|
|
709 |
< |
%\section{\label{methodSection:coarseGrained}Coarse-Grained Modeling} |
709 |
> |
After the force calculation, define $G_\alpha$ as |
710 |
> |
\begin{equation} |
711 |
> |
G_{\alpha} = \sum_i F_{\alpha i}, \label{oopseEq:zc1} |
712 |
> |
\end{equation} |
713 |
> |
where $F_{\alpha i}$ is the force in the z direction of atom $i$ in |
714 |
> |
z-constrained molecule $\alpha$. The forces of the z constrained |
715 |
> |
molecule are then set to: |
716 |
> |
\begin{equation} |
717 |
> |
F_{\alpha i} = F_{\alpha i} - |
718 |
> |
\frac{m_{\alpha i} G_{\alpha}}{\sum_i m_{\alpha i}}. |
719 |
> |
\end{equation} |
720 |
> |
Here, $m_{\alpha i}$ is the mass of atom $i$ in the z-constrained |
721 |
> |
molecule. Having rescaled the forces, the velocities must also be |
722 |
> |
rescaled to subtract out any center of mass velocity in the z |
723 |
> |
direction. |
724 |
> |
\begin{equation} |
725 |
> |
v_{\alpha i} = v_{\alpha i} - |
726 |
> |
\frac{\sum_i m_{\alpha i} v_{\alpha i}}{\sum_i m_{\alpha i}}, |
727 |
> |
\end{equation} |
728 |
> |
where $v_{\alpha i}$ is the velocity of atom $i$ in the z direction. |
729 |
> |
Lastly, all of the accumulated z constrained forces must be |
730 |
> |
subtracted from the system to keep the system center of mass from |
731 |
> |
drifting. |
732 |
> |
\begin{equation} |
733 |
> |
F_{\beta i} = F_{\beta i} - \frac{m_{\beta i} \sum_{\alpha} |
734 |
> |
G_{\alpha}} |
735 |
> |
{\sum_{\beta}\sum_i m_{\beta i}}, |
736 |
> |
\end{equation} |
737 |
> |
where $\beta$ are all of the unconstrained molecules in the system. |
738 |
> |
Similarly, the velocities of the unconstrained molecules must also |
739 |
> |
be scaled. |
740 |
> |
\begin{equation} |
741 |
> |
v_{\beta i} = v_{\beta i} + \sum_{\alpha} |
742 |
> |
\frac{\sum_i m_{\alpha i} v_{\alpha i}}{\sum_i m_{\alpha i}}. |
743 |
> |
\end{equation} |
744 |
|
|
745 |
< |
%\section{\label{methodSection:moleculeScale}Molecular-Scale Modeling} |
745 |
> |
At the very beginning of the simulation, the molecules may not be at |
746 |
> |
their constrained positions. To move a z-constrained molecule to its |
747 |
> |
specified position, a simple harmonic potential is used |
748 |
> |
\begin{equation} |
749 |
> |
U(t)=\frac{1}{2}k_{\text{Harmonic}}(z(t)-z_{\text{cons}})^{2},% |
750 |
> |
\end{equation} |
751 |
> |
where $k_{\text{Harmonic}}$ is the harmonic force constant, $z(t)$ |
752 |
> |
is the current $z$ coordinate of the center of mass of the |
753 |
> |
constrained molecule, and $z_{\text{cons}}$ is the constrained |
754 |
> |
position. The harmonic force operating on the z-constrained molecule |
755 |
> |
at time $t$ can be calculated by |
756 |
> |
\begin{equation} |
757 |
> |
F_{z_{\text{Harmonic}}}(t)=-\frac{\partial U(t)}{\partial z(t)}= |
758 |
> |
-k_{\text{Harmonic}}(z(t)-z_{\text{cons}}). |
759 |
> |
\end{equation} |