[gmx-users] single point calculation with gromacs

Justin Lemkul jalemkul at vt.edu
Wed Oct 30 16:50:44 CET 2013

On 10/30/13 9:31 AM, fantasticqhl wrote:
> Dear All,
> I want to do the single point calculations for my systems with gromacs, I
> used the method mentioned on the gmx's website.
> mdrun -s sp.tpr -rerun configuration.pdb.
> However, I have some questions on how to generate the tpr file for single
> point calculation. It didn't work if I used a mdp files of minimization to
> generate the tpr file. It worked if I used a mdp files of md in vacuum, but
> the energies were much higher than those reported by the 0-step
> minimization. I guess that there might be some problem.

Maybe this?


> Could some one give me some suggestion on the mdp file for this kind of
> single point callculations? Thanks very much!

It would help if you posted the .mdp file(s) that you're using.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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