[gmx-users] Re: Simulation of a protein in a water/DMSO box

Vitaly V. Chaban vvchaban at gmail.com
Mon Sep 28 15:23:15 CEST 2009

Hi Simone,

I would advise you to insert the needed number of waters (genbox -cp
conf.gro -cs water.gro -o conf1.gro) and then do the same with DMSO
((genbox -cp conf1.gro -cs dmso.gro -o conf2.gro). Then just


> I need to run a simulation of a protein in a water/DMSO mixture. I can't
> quite understand how should I do this... should I normally solvate the
> protein with water and then replace a certain number of water molecules
> (according to the needed % of DMSO) with DMSO molecules? But in this case,
> how should I do it? Is there a way of replacing solvent molecules with other
> solvent molecules, but of a different type?
> I'm sorry but I don't know which procedure to follow.
> Thanks in advance

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