[gmx-users] Unusual processing time

[Justin Lemkul]

On 1/3/13 9:33 PM, Xu Dong Huang wrote:
> Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 box system with water solvent + large multiple solutes.
>

Performance depends mostly on the number of atoms.  You haven't provided that 
information, so it's hard to judge what you might expect.

-Justin

> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu
>
> On Jan 3, 2013, at 9:29 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>
>> Dear gromac users,
>>
>> I submitted my NPT run into a MPI cluster. The size of my run system is an 85x85x85 box filled with water solvent. and I set NPT steps to be 1000000 (1million) with dt 0.02. The log says It will finish sometime in mid or towards end of february.
>>
>> Is that normal for a NPT run of that size? Or am I just faced with slow technology. Or am I doing something wrong (I requested 6 cores for my run)
>> Please let me know, thanks.
>>
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering
>> xudongh at eden.rutgers.edu
>>
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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