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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 16:18:22 CEST 2009

Vitaly V. Chaban wrote:
> Justin,
> 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.

Indeed, but that's not what you posted in the last message.  Just thought I'd 
make sure that was clear.  I had recommended using -maxsol earlier.  In my 
experience, it has been easier to insert one component first using -ci -nmol, 
then making use of -maxsol.


> Vitaly
> 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


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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