[gmx-users] MD simulations with multiple structures

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 21 16:46:15 CET 2010

pawan raghav wrote:
> Dear Justin,
> I want to know about
> 1. How to run MD simulations with multiple structures?

Place whatever components you need in the box with editconf, genconf, etc. and 
run the simulation.  There's really nothing special about having more than one 
structure (I'm assuming protein?) in a single unit cell.  Usually such a system 
can be built entirely with editconf - define the box, use -center, -translate, 
and/or -rotate to position your molecules and proceed.


> -- 
> Pawan


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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