[gmx-users] distance restraint

Justin Lemkul jalemkul at vt.edu
Sat Aug 8 04:41:33 CEST 2015

On 8/7/15 5:34 AM, xiao wrote:
> Dear Gromacs users,
> I am running a MD with distance restraint between two atoms. Firstly, i put the following text in the topology file:
> [distance_restraints]
> 230 1683 1 0 1 0.25 0.27 0.29 50
> This is to restraint the distance between the two atoms 230 and 1683 around 0.26 nm. I am not sure the units used by Gromacs, and i guess it is nanometer, can anyone tell me whether i am right or not?

Chapter 2 of the manual will tell you if you're right or not.

> Secondly, i added the following text in the .mdp file:
> disre_fc=100
> disre=simple
> This is what i did, and i am not sure whether i skip something important. I really appreciate it to get any information from you.

Did you obtain the expected restraint?



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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