[gmx-users] removal of water
jalemkul at vt.edu
Tue Oct 16 15:36:46 CEST 2012
On 10/16/12 7:46 AM, Shine A wrote:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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