[gmx-users] How to have two proteins randomly positioned and oriented in the box

Justin Lemkul jalemkul at vt.edu
Mon Apr 1 04:21:17 CEST 2013

On 3/31/13 9:51 PM, Zhikun Cai wrote:
> Hi everyone,
> I am trying to insert two same proteins in a simulation box. Now I have
> used pdb2gmx to convert one protein's pdb file to gro file. Then how should
> I do? How could they be randomly positioned and oriented in the box?

Place them however you like within the box using editconf -center, -translate, 
-rotate, etc as necessary.  You may be able to get completely random insertion 
with genbox -ci -nmol, but I've never tried it with a protein.



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


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