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

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 28 14:00:18 CEST 2009

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.


> Simone Cirri
> simonecirri at gmail.com <mailto:simonecirri at gmail.com>
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list