[gmx-users] Make DNA stay in the center of the box during Simulation

Justin Lemkul jalemkul at vt.edu
Sat Dec 6 15:08:53 CET 2014

On 12/6/14 5:13 AM, Hovakim Grabski wrote:
> Dear Gromacs users,I'm trying to run a simulation between a DNA(12 base pair) and 6 molecules of methylene blue,is there any effective way to make the DNA stay in the center of the box during md simulation?

In a periodic system, there is no such thing as a "center."  There is no 
productive reason to enforce such a restriction during the simulation like this. 
  The molecules are going to diffuse around.  If they are capable of 
interacting, they will do just that over the course of the simulation, 
irrespective of whatever convenient visualization convention you may wish to have.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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