From: Carsten Kutzner Date: Thu, 13 Feb 2014 17:08:23 +0000 (+0100) Subject: Small enhancement of computational electrophysiology manual section. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=423b5001540ff9e4a8695b1bd1496e58e8824ee2;p=alexxy%2Fgromacs.git Small enhancement of computational electrophysiology manual section. Added a note about what can be done if large membrane undulations turn out to be a problem in a Computational Electrophysiology setup. Change-Id: I5f50b4026ea1a8b88368b10c39d2207070c4740c --- diff --git a/manual/special.tex b/manual/special.tex index d77fef7a95..621b9a2d4d 100644 --- a/manual/special.tex +++ b/manual/special.tex @@ -1137,6 +1137,11 @@ is the box length in that direction. If you have already defined index groups fo the channel for the single-layered system, {\tt gmx make_ndx -n index.ndx -twin} will provide you with the groups for the double-layered system. +To suppress large fluctuations of the membranes along the swap direction, +it may be useful to apply a harmonic potential (acting only in the swap dimension) +between each of the two channel and/or bilayer centers using umbrella pulling +(see section~\ref{sec:pull}). + \subsection*{Multimeric channels} If a split group consists of more than one molecule, the correct PBC image of all molecules with respect to each other has to be chosen such that the channel center can be correctly