[gmx-users] Unusual processing time

[Xu Dong Huang]

The average of all my variations contain about 802780 atoms. 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 3, 2013, at 9:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> 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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