[gmx-users] simulating several proteins

Mark Abraham mark.abraham at anu.edu.au
Wed Mar 10 16:27:19 CET 2010

----- Original Message -----
From: Cristiano De Michele <cristiano.demichele at roma1.infn.it>
Date: Thursday, March 11, 2010 2:25
Subject: [gmx-users] simulating several proteins
To: gmx-users at gromacs.org

> Dear all,
> is it possible to simulate more than one protein with GROMACS?
> I would like to simulate two lysozyme proteins not solvated and
> I tried changing number of proteins in topology file (attached) and
> then I used this modified .top file to generate a .gro configuration
> with genbox, but I always end up getting just one protein
> in the simulation box...

genbox doesn't take input from the .top file to guide its output.

Use genconf on your original structure file to multiply it. Then edit your .top by hand to match.


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