[gmx-users] electrical potential using Gromacs

Justin Lemkul jalemkul at vt.edu
Mon Jan 6 17:11:13 CET 2014

On 1/4/14, 12:00 PM, Andrew DeYoung wrote:
> Hi,
> I was able to "fix" the drift in the electric potential by using particle
> decomposition parallelization instead of domain decomposition when running
> the simulations using mdrun (although I still do not know why this "fixes"
> the problem).  Domain decomposition is the default parallelization in
> Gromacs, but particle decomposition can be used with the -pd switch of
> mdrun.  However, I think that particle decomposition is slated to be removed
> in future versions of Gromacs.

Given that there seems to be a problem with DD, I have opened a Redmine issue:


If you would like to add input files that reproduce the problem, that would help 
in arriving at a solution.



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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