[gmx-users] Using several cores for MD production

[Dr. Vitaly Chaban]

The invocation line depends on the MPI tool installed on the cluster.

E.g. in case of openmpi, you write
openmpi -np 64 mdrun -dd 4 4 4


Dr. Vitaly V. Chaban


On Tue, Dec 3, 2013 at 4:58 PM, MUSYOKA THOMMAS
<mutemibiochemistry at gmail.com> wrote:
> Dear Justin,
> Well it seems i am the first one to do MD simulations in my lab and i am
> using a chemistry department cluster and nobody has prior knowledge on
> GROMACS. I can use all the cores in the cluster but need to know if there
> is a specific mdrun command that can allow me specify the number of cores
> to be used for the MD run.
>
> Thank you
>
>
> On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote:
>>
>>> Dear Users,
>>>
>>> I am using a cluster of 64 cores to perform my MD simulations using
>>> GROMACS
>>> version 4.5.5.
>>>
>>> I would be glad to know the exact mdrun command that will allow me use the
>>> available resources.
>>>
>>>
>> The answer depends entirely on the architecture of the cluster.  Your sys
>> admin should know.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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> *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540*
> *B.Sc Biochemistry (Kenyatta University), MSc Pharmaceutical Science
> (Nagasaki University)*
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