| 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. |
| 876 |
> |
ensemble using a Nos\'e-Hoover thermostat, six |
| 877 |
> |
statistically-independent replicas of this liquid-phase system were |
| 878 |
> |
run in the microcanonical (NVE) ensemble under the Ewald, Hard, SP, |
| 879 |
> |
GSF, and TSF methods with a cutoff radius of 12~\AA. The value of the |
| 880 |
> |
damping coefficient was also varied from the undamped case ($\alpha = |
| 881 |
> |
0$) to a heavily damped case ($\alpha = 0.3$~\AA$^{-1}$) for all of |
| 882 |
> |
the real space methods. A sample was also run using the multipolar |
| 883 |
> |
Ewald sum with the same real-space cutoff. |
| 884 |
|
|
| 885 |
|
In figure~\ref{fig:energyDrift} we show the both the linear drift in |
| 886 |
|
energy over time, $\delta E_1$, and the standard deviation of energy |
| 901 |
|
|
| 902 |
|
\begin{figure} |
| 903 |
|
\centering |
| 904 |
< |
\includegraphics[width=\textwidth]{newDrift_12.eps} |
| 904 |
> |
\includegraphics[width=\textwidth]{finalDrift.eps} |
| 905 |
|
\caption{Energy conservation of the real-space methods for the soft |
| 906 |
< |
DQ liauid / ion system. $\delta \mathrm{E}_1$ is the linear drift |
| 906 |
> |
DQ liquid / ion system. $\delta \mathrm{E}_1$ is the linear drift |
| 907 |
|
in energy over time (in kcal/mol/particle/ns) and $\delta |
| 908 |
|
\mathrm{E}_0$ is the standard deviation of energy fluctuations |
| 909 |
|
around this drift (in kcal/mol/particle). Points that appear in |
