| 150 |
|
increasing time step. For each time step, the dotted line is total |
| 151 |
|
energy using the DLM integrator, and the solid line comes from the |
| 152 |
|
quaternion integrator. The larger time step plots are shifted up |
| 153 |
< |
from the true energy baseline for clarity.} \label{timestep} |
| 153 |
> |
from the true energy baseline for clarity.} |
| 154 |
> |
\label{methodFig:timestep} |
| 155 |
|
\end{figure} |
| 156 |
|
|
| 157 |
< |
In Fig.~\ref{timestep}, the resulting energy drift at various time |
| 158 |
< |
steps for both the DLM and quaternion integration schemes is |
| 159 |
< |
compared. All of the 1000 molecule water simulations started with |
| 160 |
< |
the same configuration, and the only difference was the method for |
| 161 |
< |
handling rotational motion. At time steps of 0.1 and 0.5 fs, both |
| 162 |
< |
methods for propagating molecule rotation conserve energy fairly |
| 163 |
< |
well, with the quaternion method showing a slight energy drift over |
| 164 |
< |
time in the 0.5 fs time step simulation. At time steps of 1 and 2 |
| 165 |
< |
fs, the energy conservation benefits of the DLM method are clearly |
| 166 |
< |
demonstrated. Thus, while maintaining the same degree of energy |
| 167 |
< |
conservation, one can take considerably longer time steps, leading |
| 168 |
< |
to an overall reduction in computation time. |
| 157 |
> |
In Fig.~\ref{methodFig:timestep}, the resulting energy drift at |
| 158 |
> |
various time steps for both the DLM and quaternion integration |
| 159 |
> |
schemes is compared. All of the 1000 molecule water simulations |
| 160 |
> |
started with the same configuration, and the only difference was the |
| 161 |
> |
method for handling rotational motion. At time steps of 0.1 and 0.5 |
| 162 |
> |
fs, both methods for propagating molecule rotation conserve energy |
| 163 |
> |
fairly well, with the quaternion method showing a slight energy |
| 164 |
> |
drift over time in the 0.5 fs time step simulation. At time steps of |
| 165 |
> |
1 and 2 fs, the energy conservation benefits of the DLM method are |
| 166 |
> |
clearly demonstrated. Thus, while maintaining the same degree of |
| 167 |
> |
energy conservation, one can take considerably longer time steps, |
| 168 |
> |
leading to an overall reduction in computation time. |
| 169 |
|
|
| 170 |
|
\subsection{\label{methodSection:NVT}Nos\'{e}-Hoover Thermostatting} |
| 171 |
|
|
| 172 |
< |
The Nos\'e-Hoover equations of motion are given by\cite{Hoover85} |
| 172 |
> |
The Nos\'e-Hoover equations of motion are given by\cite{Hoover1985} |
| 173 |
|
\begin{eqnarray} |
| 174 |
|
\dot{{\bf r}} & = & {\bf v}, \\ |
| 175 |
|
\dot{{\bf v}} & = & \frac{{\bf f}}{m} - \chi {\bf v} ,\\ |
| 285 |
|
|
| 286 |
|
The Nos\'e-Hoover algorithm is known to conserve a Hamiltonian for |
| 287 |
|
the extended system that is, to within a constant, identical to the |
| 288 |
< |
Helmholtz free energy,\cite{melchionna93} |
| 288 |
> |
Helmholtz free energy,\cite{Melchionna1993} |
| 289 |
|
\begin{equation} |
| 290 |
|
H_{\mathrm{NVT}} = V + K + f k_B T_{\mathrm{target}} \left( |
| 291 |
|
\frac{\tau_{T}^2 \chi^2(t)}{2} + \int_{0}^{t} \chi(t^\prime) |
| 295 |
|
$H_{\mathrm{NVT}}$, so the conserved quantity is maintained in the |
| 296 |
|
last column of the {\tt .stat} file to allow checks on the quality |
| 297 |
|
of the integration. |
| 297 |
– |
|
| 298 |
– |
Bond constraints are applied at the end of both the {\tt moveA} and |
| 299 |
– |
{\tt moveB} portions of the algorithm. Details on the constraint |
| 300 |
– |
algorithms are given in section \ref{oopseSec:rattle}. |
| 298 |
|
|
| 299 |
|
\subsection{\label{methodSection:NPTi}Constant-pressure integration with |
| 300 |
|
isotropic box deformations (NPTi)} |
| 301 |
|
|
| 302 |
|
To carry out isobaric-isothermal ensemble calculations {\sc oopse} |
| 303 |
|
implements the Melchionna modifications to the |
| 304 |
< |
Nos\'e-Hoover-Andersen equations of motion,\cite{melchionna93} |
| 304 |
> |
Nos\'e-Hoover-Andersen equations of motion,\cite{Melchionna1993} |
| 305 |
|
|
| 306 |
|
\begin{eqnarray} |
| 307 |
|
\dot{{\bf r}} & = & {\bf v} + \eta \left( {\bf r} - {\bf R}_0 \right), \\ |
