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 |
|
|
752 |
|
time was provided by the Center for Research Computing (CRC) at the |
753 |
|
University of Notre Dame. |
754 |
|
|
755 |
+ |
Molecular graphics images were produced using the UCSF Chimera package from |
756 |
+ |
the Resource for Biocomputing, Visualization, and Informatics at the |
757 |
+ |
University of California, San Francisco (supported by NIH P41 RR001081). |
758 |
|
\newpage |
759 |
|
|
760 |
|
\bibliography{langevinHull} |