[gmx-users] removal of water

Justin Lemkul jalemkul at vt.edu
Tue Oct 16 15:36:46 CEST 2012

On 10/16/12 7:46 AM, Shine A wrote:
> Sir,
>     I am studying the dynamics of membrane proteins using KALP-15 in DPPC.I
> solvated  the system using
>   genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro  .
> But system_shrink1_solv.gro contain some unwanted water molecules in
> between lipid. How to eliminate these water molecules?plz help.

You should not add water until the system is completely packed.  Otherwise you 
just end up with a system with a huge amount of atoms in incorrect locations.
Generally, one can remove unwanted waters rather easily:


But I would still suggest you re-evaluate your approach.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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