[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?

http://redmine.gromacs.org/issues/1341

> 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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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