[gmx-users] Adding water to a lipid bilayer

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 3 07:46:35 CET 2009

krithika krishnaswamy wrote:
> 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

Start here: http://wiki.gromacs.org/index.php/Membrane_Simulations


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