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

Vitaly V. Chaban vvchaban at gmail.com
Mon Sep 28 16:14:24 CEST 2009


Simeone will insert only "the needed number of waters" but not the
full box. :)  To do so he will use an option "-maxsol XXX" of genbox.


On Mon, Sep 28, 2009 at 5:08 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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.
> -Justin
>> 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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