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