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

[Justin A. Lemkul]

Simone Cirri wrote:
> Hi everyone,
> 
> 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
> 

The easiest way I can think of is to define the box around your protein, use 
genbox -ci -nmol to insert the desired number of DMSO molecules, and then fill 
the box with water.  You may have to tweak the box size or use genbox -maxsol to 
get the desired concentration.

-Justin

> Simone Cirri
> 
> simonecirri at gmail.com <mailto:simonecirri at gmail.com>
> 
> 
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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