[gmx-users] confusion about implicint solvent

Justin Lemkul jalemkul at vt.edu
Mon Sep 23 20:23:35 CEST 2013

On 9/23/13 2:08 PM, Szilárd Páll wrote:
> Hi,
> Admittedly, both the documentation on these features and the
> communication on the known issues with these aspects of GROMACS has
> been lacking.
> Here's a brief summary/explanation:
> - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu
> which is essentially mdrun + OpenMM, hence it has some limitations,
> most notably it can only run on a single GPU. The performance,
> depending on setting, can be up to 10x higher than on the CPU.
> - GROMACS 4.6: the native GPU acceleration does supports only explicit
> solvent, mdrun + OpenMM is still available (exactly for implicit
> solvent runs), but has been moved to the "contrib" section which means
> that it is not fully supported. Moreover, OpenMM support - unless
> somebody volunteers for maintenance of the mdrun-OpenMM interface -
> will be dropped in the next release.
> I can't comment much on the implicit solvent code on the CPU side
> other than the fact that there have been issues which AFAIK limit the
> parallelization to a rather small number of cores, hence the
> achievable performance is also limited. I hope others can clarify this
> aspect.

I never got the implicit code to run on more than 2 CPUs, and as I recall Berk 
hard-coded this due to a limitation involving constraints.  It's been a couple 
years since I tried anything with implicit since (1) the OpenMM support was so 
buggy and incomplete on GPU and (2) the code ran an order of magnitude slower on 
CPU than the explicit solvent counterpart.



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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