[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

Justin Lemkul jalemkul at vt.edu
Tue May 24 14:35:36 CEST 2016

On 5/24/16 6:35 AM, Antara mazumdar wrote:
> Dear gromacs users,
> I am trying to calculate domain decomposition of a mixed lipid vesicle
> system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to
> run in parallel.
> I want to calculate the number of PME nodes per total number of nodes.
> However, i am not clear on how to calculate the value of nPME here. I would
> also mention that number of nodes that can be used need to be multiple of
> 16 and the value of minimum cell size is 1.8 nm.
> Can someone guide me in this regard?

Is there something wrong with the number of PME nodes that mdrun sets up by default?



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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