[gmx-users] Bad water removal

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 7 19:19:26 CEST 2011

madhumita das wrote:
> Hi, 
>  I have generated a membrane protein complex and then added a waterbox 
> using Gromacs,but instead of being at the outer surfaces of lipid 
> membrane,water spreads all around the membrane. How to make appropriate 
> water box?am I doing a simple mistake?

If you've got water all around the membrane, then your box dimensions are 
probably set incorrectly.

Please see the following tutorial; it addresses this issue and others:




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


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