[gmx-users] problem regarding removal of water from final simulation system.

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 11 07:22:41 CEST 2009

nitu sharma wrote:
> Dear all
>  I have done successfully simulation of membrane protein , but after 
> that to visualise my final model clearly I have to remove water 
> molecules from my system (protein+lipid+water).
> But  I have no Idea about the which command I should use to do this even 
> it doesn't mentioned in justin,s tutorial also to make final pdb after 
> simulation.
> So can anyone suggest me  how to remove water form my final simulation 
> system to make final pdb of only protein and lipid molecule?

You asked a very similar question a few days ago, which I answered then. 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042525.html You 
want to extract a non-standard group (i.e. non-solvent), so you need to 
make an index file that defines that group.


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