[gmx-users] vacuum/gas md

Justin Lemkul jalemkul at vt.edu
Sat Feb 20 20:26:59 CET 2016

On 2/20/16 1:49 PM, Rasha Alqus wrote:
> Dear Gromacs users,
> I have performed PMF calculation for my system in water at npt, I ran them on GPU .
> Now I wish to run them in gas phase and compare them with the waters and I have some questions:
> To run in gas I should place pbc=no rlist=rcoulomb=rvdw=0. The GPU only support the cutoff-scheme = verlet  and the pbc should be xyz or xy. Is it okay to use cutoff-scheme=Group and they will run on CPU not GPU?Any other advices on what to use?

Correct, such runs can only be done on CPU.

> If any can provide me with  input mdp for simulation in vacuum would be very helpful.

You've already listed the most important changes above.



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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