| 611 |
|
|
| 612 |
|
\subsection{\label{methodSection:otherSpecialEnsembles}Other Special Ensembles} |
| 613 |
|
|
| 614 |
< |
\subsubsection{\label{methodSection:NPAT}Constant Normal Pressure, Constant Lateral Surface Area and Constant Temperature (NPAT) Ensemble} |
| 614 |
> |
\subsubsection{\label{methodSection:NPAT}NPAT Ensemble} |
| 615 |
|
|
| 616 |
|
A comprehensive understanding of structure¨Cfunction relations of |
| 617 |
|
biological membrane system ultimately relies on structure and |
| 633 |
|
Note that the iterative schemes for NPAT are identical to those |
| 634 |
|
described for the NPTi integrator. |
| 635 |
|
|
| 636 |
< |
\subsubsection{\label{methodSection:NPrT}Constant Normal Pressure, Constant Lateral Surface Tension and Constant Temperature (NP\gamma T) Ensemble } |
| 636 |
> |
\subsubsection{\label{methodSection:NPrT}NP$\gamma$T Ensemble} |
| 637 |
|
|
| 638 |
|
Theoretically, the surface tension $\gamma$ of a stress free |
| 639 |
|
membrane system should be zero since its surface free energy $G$ is |
| 643 |
|
\] |
| 644 |
|
However, a surface tension of zero is not appropriate for relatively |
| 645 |
|
small patches of membrane. In order to eliminate the edge effect of |
| 646 |
< |
the membrane simulation, a special ensemble, NP\gamma T, is proposed |
| 647 |
< |
to maintain the lateral surface tension and normal pressure. The |
| 648 |
< |
equation of motion for cell size control tensor, $\eta$, in NP\gamma |
| 649 |
< |
T is |
| 646 |
> |
the membrane simulation, a special ensemble, NP$\gamma$T, is |
| 647 |
> |
proposed to maintain the lateral surface tension and normal |
| 648 |
> |
pressure. The equation of motion for cell size control tensor, |
| 649 |
> |
$\eta$, in NP\gamma T is |
| 650 |
|
\begin{equation} |
| 651 |
|
\dot |
| 652 |
|
\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\leftrightarrow$}} |
| 674 |
|
integrator is a special case of $NP\gamma T$ if the surface tension |
| 675 |
|
$\gamma$ is set to zero. |
| 676 |
|
|
| 677 |
+ |
%\section{\label{methodSection:constraintMethod}Constraint Method} |
| 678 |
+ |
|
| 679 |
+ |
%\subsection{\label{methodSection:bondConstraint}Bond Constraint for Rigid Body} |
| 680 |
+ |
|
| 681 |
+ |
%\subsection{\label{methodSection:zcons}Z-constraint Method} |
| 682 |
+ |
|
| 683 |
|
\section{\label{methodSection:langevin}Integrators for Langevin Dynamics of Rigid Bodies} |
| 684 |
|
|
| 685 |
|
\subsection{\label{methodSection:temperature}Temperature Control} |
