--- trunk/tengDissertation/Methodology.tex 2006/06/11 02:06:01 2851 +++ trunk/tengDissertation/Methodology.tex 2006/06/11 02:23:00 2853 @@ -356,11 +356,7 @@ relaxation of the pressure to the target value. To se \end{equation} In eq.(\ref{eq:melchionna1}), $\tau_B$ is the time constant for -relaxation of the pressure to the target value. To set values for -$\tau_B$ or $P_{\mathrm{target}}$ in a simulation, one would use the -{\tt tauBarostat} and {\tt targetPressure} keywords in the {\tt -.bass} file. The units for {\tt tauBarostat} are fs, and the units -for the {\tt targetPressure} are atmospheres. Like in the NVT +relaxation of the pressure to the target value. Like in the NVT integrator, the integration of the equations of motion is carried out in a velocity-Verlet style 2 part algorithm: @@ -472,9 +468,6 @@ P_{\mathrm{target}} \mathcal{V}(t). \left( \chi^2 \tau_T^2 + \eta^2 \tau_B^2 \right) + P_{\mathrm{target}} \mathcal{V}(t). \end{equation} - -Bond constraints are applied at the end of both the {\tt moveA} and -{\tt moveB} portions of the algorithm. \subsection{\label{methodSection:NPTf}Constant-pressure integration with a flexible box (NPTf)}