[gmx-users] About Binary mixture

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 31 20:17:49 CEST 2009

Abhishek Banerjee wrote:
> Hi all,
>           Actually I want simulate some binary liquid mixture like DMF 
> and methanol and just want to find diffusion coefficient for each of the 
> components. But the problem is I am not able to create DMF solvent box. 
> I have created the .itp and .pdb file of DMF from 
> http://davapc1.bioch.dundee.ac.uk/prodrg/. I am new to gromacs. If 
> someone kindly give me some advice, will be helpful for me.

The first thing to know is that you should not necessarily trust the PRODRG 
topology at face value.  Validate its parameters using methodology compatible 
with the force field you intend to use.  See here:


To construct the system, genbox is your friend.  Use genbox -ci -nmol -box to 
insert the solute into the unit cell, and fill the box with the solvent, also 
using genbox.  If you need to create a solvent box from which to start, that is 
also done with genbox, either using -ci -nmol or -maxsol.  The documentation 
explains each of these options.


> Thanking you
> abhishek
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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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