[gmx-users] removal of water

[Justin Lemkul]

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:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations

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

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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