[gmx-users] Vacuum simulation in GMX 5

Justin Lemkul jalemkul at vt.edu
Thu May 7 14:49:39 CEST 2015

On 5/7/15 8:43 AM, Eudes Fileti wrote:
> Justin, thanks for the help.
> Originally I have tried the options you suggested, and the GMX 5 not
> accepted well, since there are not more -pd option, which allowed to
> perform the calculation with pbc = no.

Well, technically it allows you to run in parallel via PD with no PBC. 
Parallelization is not mandatory and usually small vacuum systems do not benefit 
from running in parallel (usually performance degrades when you have few atoms).

> So, you asked me to see my input. The first test I did was obviously
> considering cut-offs, since I needed impose pbc = yes. These parameters are
> the ones I sent you.

pbc = xyz is not an in vacuo simulation.

> Of course plain cutoffs is not dealing well with the electrostatic part,
> but in this case I was only doing just a quick test.
> You said you have made calculations for a molecule of 50 atoms at a rate of
> 130ns/day on a single core. Did you used to that Gromacs 5? What are the
> mdp options that you use in this case?

Yes, version 5.0, using exactly the settings I posted.



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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