[gmx-users] Adding water to a lipid bilayer

krithika krishnaswamy krithika.bioinfo at gmail.com
Sat Jan 3 07:19:37 CET 2009

Am a new user to gromacs and am making a comparitive study of different
bilayer simulation.For the other two bilayers i took pre-equilibriated
system and ran the simulation.Now for one of the bilayer am trying to make
it of my own.

I tried to remove water,by first adding water to entire system and then
removed water from sides using a tcl script.But since this system is huge,am
getting error with this procedure.

My query is,*how will you add water to the bilayer so that water should not
be in the middle & sides of the bilayer.*Is there something that can be
specified in the genbox command so that i can add water to that layer alone
and build layer by layer.Am damn confused.Please provid a solution for this
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