--- trunk/tengDissertation/Methodology.tex 2006/05/26 17:56:36 2778 +++ trunk/tengDissertation/Methodology.tex 2006/06/06 14:12:59 2798 @@ -621,15 +621,16 @@ standard NPT ensemble with a different pressure contro called the average surface area per lipid. Constat area and constant lateral pressure simulation can be achieved by extending the standard NPT ensemble with a different pressure control strategy + \begin{equation} -\dot -\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\leftrightarrow$}} -\over \eta } _{\alpha \beta } = \left\{ \begin{array}{l} - \frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau _{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}} }}{\rm{ }}(\alpha = \beta = z), \\ - 0{\rm{ }}(\alpha \ne z{\rm{ }}or{\rm{ }}\beta \ne z) \\ - \end{array} \right. -\label{methodEquation:NPATeta} + \.{\overleftrightarrow{{\eta _{\alpha \beta}}}}=\left\{\begin{array}{ll} + \frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau_{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}} }} + & \mbox{if \[ \alpha = \beta = z)$}\\ + 0 & \mbox{otherwise}\\ + \end{array} + \right. \end{equation} + Note that the iterative schemes for NPAT are identical to those described for the NPTi integrator. @@ -648,14 +649,11 @@ $\eta$, in $NP\gamma T$ is pressure. The equation of motion for cell size control tensor, $\eta$, in $NP\gamma T$ is \begin{equation} -\dot -\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\leftrightarrow$}} -\over \eta } _{\alpha \beta } = \left\{ \begin{array}{l} - - A_{xy} (\gamma _\alpha - \gamma _{{\rm{target}}} ){\rm{ (}}\alpha = \beta = x{\rm{ or }} = y{\rm{)}} \\ - \frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau _{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}} }}{\rm{ }}(\alpha = \beta = z) \\ - 0{\rm{ }}(\alpha \ne \beta ) \\ - \end{array} \right. -\label{methodEquation:NPrTeta} + \.{\overleftrightarrow{{\eta _{\alpha \beta}}}}=\left\{\begin{array}{ll} + - A_{xy} (\gamma _\alpha - \gamma _{{\rm{target}}} ) & \mbox{$\alpha = \beta = x$ or $\alpha = \beta = y$}\\ + \frac{{V(P_{\alpha \beta } - P_{{\rm{target}}} )}}{{\tau _{\rm{B}}^{\rm{2}} fk_B T_{{\rm{target}}}}} & \mbox{$\alpha = \beta = z$} \\ + 0 & \mbox{$\alpha \ne \beta$} \\ + \right. \end{equation} where $ \gamma _{{\rm{target}}}$ is the external surface tension and the instantaneous surface tensor $\gamma _\alpha$ is given by