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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 16:08:48 CEST 2009

Vitaly V. Chaban wrote:
> 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
> equilibrate.

I doubt that will work.  The first call to genbox there will fill the box with 
water, leaving no room for anything else.


> Vitaly
>> 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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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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