[gmx-users] using more processors for g_mindist

[Mark Abraham]

On 29/02/2012 6:01 PM, aiswarya pawar wrote:
> Mark,
>
> Right now am computing distance between each protein atom against all 
> water atoms,

That's expensive. mdrun goes to great lengths to speed up computing 
billions of distances.

> which is taking too long for 5ns run. i cant reduce the frames

Yes you can. Even if you think you need data from every frame, you 
probably don't because they're correlated with each other, and at the 
very least you can do a pilot study on a frame every 100ps or every 
nanosecond before committing to one on all the frames.

> either the number of water atoms. So is there any alternate.
>

You are not likely to get a better solution if you only describe your 
attempt, rather than describe the objective. Asking "how do I hammer 
harder?" if you're hammering a screw makes it impossible to get the 
correct solution "Use a screwdriver".

Mark

> Thanks
>
> On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 29/02/2012 5:17 PM, aiswarya pawar wrote:
>>     Dear all,
>>
>>     Am running g_mindist on large number of atoms, i would like to
>>     know whether i can run this on more than one processors say 8
>>     processors to speed up the task?
>
>     No. If it will take too long, you need to reduce your number of
>     frames (trjconv), or the number of atoms (also trjconv), or some such.
>
>     Mark
>
>
>>     and will this effect the output in anyways.
>>
>>     Thanks,
>>
>>     -- 
>>     Aiswarya  B Pawar
>>
>>
>>
>>
>
>
>     --
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>
>
>
> -- 
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>

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