[gmx-users] Performance drops when simulating protein with small ligands

[Justin Lemkul]

On 3/20/15 1:13 PM, Yunlong Liu wrote:
> Hi,
>
> I am running my protein with two ligands. Both ligands are small molecules like
> ATP. However, my simulation performance drops a lot by adding this two ligands
> with the same set of other parameters.
>
> Previously with ligands, I have 30 ns/day with 64-cpus and 4gpus. But now I can
> only gain 17 ns/day with the same setting. I want to know whether this is a
> common phenomenon or I do something stupid.
>

Probably some other process is using resources and degrading your performance, 
or you're using different run settings (the .log file is definitive here).  The 
mere addition of ligands does not degrade performance.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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