| 40 |
|
We have developed a new isobaric-isothermal (NPT) algorithm which |
| 41 |
|
applies an external pressure to the facets comprising the convex |
| 42 |
|
hull surrounding the system. A Langevin thermostat is also applied |
| 43 |
< |
to facets of the hull to mimic contact with an external heat |
| 44 |
< |
bath. This new method, the ``Langevin Hull'', performs better than |
| 45 |
< |
traditional affine transform methods for systems containing |
| 46 |
< |
heterogeneous mixtures of materials with different |
| 47 |
< |
compressibilities. It does not suffer from the edge effects of |
| 48 |
< |
boundary potential methods, and allows realistic treatment of both |
| 49 |
< |
external pressure and thermal conductivity to an implicit solvent. |
| 50 |
< |
We apply this method to several different systems including bare |
| 51 |
< |
metal nanoparticles, nanoparticles in an explicit solvent, as well |
| 52 |
< |
as clusters of liquid water. The predicted mechanical properties of |
| 53 |
< |
these systems are in good agreement with experimental data and |
| 54 |
< |
previous simulation work. |
| 43 |
> |
to the facets to mimic contact with an external heat bath. This new |
| 44 |
> |
method, the ``Langevin Hull'', can handle heterogeneous mixtures of |
| 45 |
> |
materials with different compressibilities. These are systems that |
| 46 |
> |
are problematic for traditional affine transform methods. The |
| 47 |
> |
Langevin Hull does not suffer from the edge effects of boundary |
| 48 |
> |
potential methods, and allows realistic treatment of both external |
| 49 |
> |
pressure and thermal conductivity due to the presence of an implicit |
| 50 |
> |
solvent. We apply this method to several different systems |
| 51 |
> |
including bare metal nanoparticles, nanoparticles in an explicit |
| 52 |
> |
solvent, as well as clusters of liquid water. The predicted |
| 53 |
> |
mechanical properties of these systems are in good agreement with |
| 54 |
> |
experimental data and previous simulation work. |
| 55 |
|
\end{abstract} |
| 56 |
|
|
| 57 |
|
\newpage |
| 115 |
|
pressure conditions. The use of periodic boxes to enforce a system |
| 116 |
|
volume requires either effective solute concentrations that are much |
| 117 |
|
higher than desirable, or unreasonable system sizes to avoid this |
| 118 |
< |
effect. For example, calculations using typical hydration shells |
| 118 |
> |
effect. For example, calculations using typical hydration boxes |
| 119 |
|
solvating a protein under periodic boundary conditions are quite |
| 120 |
< |
expensive. [CALCULATE EFFECTIVE PROTEIN CONCENTRATIONS IN TYPICAL |
| 121 |
< |
SIMULATIONS] |
| 120 |
> |
expensive. A 62 $\AA^3$ box of water solvating a moderately small |
| 121 |
> |
protein like hen egg white lysozyme (PDB code: 1LYZ) yields an |
| 122 |
> |
effective protein concentration of 100 mg/mL.\cite{Asthagiri20053300} |
| 123 |
> |
|
| 124 |
> |
Typically protein concentrations in the cell are on the order of |
| 125 |
> |
160-310 mg/ml,\cite{Brown1991195} and the factor of 20 difference |
| 126 |
> |
between simulations and the cellular environment may have significant |
| 127 |
> |
effects on the structure and dynamics of simulated protein structures. |
| 128 |
|
|
| 129 |
+ |
|
| 130 |
|
\subsection*{Boundary Methods} |
| 131 |
|
There have been a number of approaches to handle simulations of |
| 132 |
|
explicitly non-periodic systems that focus on constant or |
| 709 |
|
\begin{enumerate} |
| 710 |
|
\item Each processor computes the convex hull for its own atomic sites |
| 711 |
|
(left panel in Fig. \ref{fig:parallel}). |
| 712 |
< |
\item The Hull vertices from each processor are passed out to all of |
| 712 |
> |
\item The Hull vertices from each processor are communicated to all of |
| 713 |
|
the processors, and each processor assembles a complete list of hull |
| 714 |
|
sites (this is much smaller than the original number of points in |
| 715 |
|
the point cloud). |
| 725 |
|
computation, the processors first compute the convex hulls for their |
| 726 |
|
own sites (dashed lines in left panel). The positions of the sites |
| 727 |
|
that make up the subset hulls are then communicated to all |
| 728 |
< |
processors (middle panel). The convex hull of the system (solid line in right panel) is the convex hull of the points on the union of the subset hulls.} |
| 728 |
> |
processors (middle panel). The convex hull of the system (solid line in |
| 729 |
> |
right panel) is the convex hull of the points on the union of the subset |
| 730 |
> |
hulls.} |
| 731 |
|
\label{fig:parallel} |
| 732 |
|
\end{figure} |
| 733 |
|
|
