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

[Justin Lemkul]

On 3/20/15 2:32 PM, Yunlong Liu wrote:
> Hi Justin,
>
> I am running this simulation on Stampede/TACC. I don't think there are other processes running on the nodes assigned to me. This is a little weird.
>

Well, as I said, the .log files will be the definitive source of run settings 
and configuration.  Look for differences.  If there are none, take it up with 
the cluster admins.  If predictable behavior is not being observed, it's worth 
looking into.  Maybe a node is simply having issues.

-Justin

> Yunlong
>> On Mar 20, 2015, at 2:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> 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
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================