[gmx-users] using more processors for g_mindist

[aiswarya pawar]

Mark,

i want to know which water atoms stay within a cut off to protein atom. ie
i need the duration at which a water resides on the protein atoms. so for
that i need the whole 5ns frames because am looking for water molecules
which reside more than 50% of time.

Thanks

On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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
>
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
Aiswarya  B Pawar

Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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