| 356 |
|
\end{equation} |
| 357 |
|
|
| 358 |
|
In eq.(\ref{eq:melchionna1}), $\tau_B$ is the time constant for |
| 359 |
< |
relaxation of the pressure to the target value. To set values for |
| 360 |
< |
$\tau_B$ or $P_{\mathrm{target}}$ in a simulation, one would use the |
| 361 |
< |
{\tt tauBarostat} and {\tt targetPressure} keywords in the {\tt |
| 362 |
< |
.bass} file. The units for {\tt tauBarostat} are fs, and the units |
| 363 |
< |
for the {\tt targetPressure} are atmospheres. Like in the NVT |
| 359 |
> |
relaxation of the pressure to the target value. Like in the NVT |
| 360 |
|
integrator, the integration of the equations of motion is carried |
| 361 |
|
out in a velocity-Verlet style 2 part algorithm: |
| 362 |
|
|
| 468 |
|
\left( \chi^2 \tau_T^2 + \eta^2 \tau_B^2 \right) + |
| 469 |
|
P_{\mathrm{target}} \mathcal{V}(t). |
| 470 |
|
\end{equation} |
| 475 |
– |
|
| 476 |
– |
Bond constraints are applied at the end of both the {\tt moveA} and |
| 477 |
– |
{\tt moveB} portions of the algorithm. |
| 471 |
|
|
| 472 |
|
\subsection{\label{methodSection:NPTf}Constant-pressure integration with a |
| 473 |
|
flexible box (NPTf)} |
