[gmx-users] using more processors for g_mindist

[Mark Abraham]

On 29/02/2012 7:21 PM, aiswarya pawar wrote:
> Mark,
>
> i want to know which water atoms stay within a cut off to protein atom.

OK, but as you will read in g_mindist -h, it will count such atoms and 
not identify which they were...

> ie i need the duration at which a water resides on the protein atoms.

... and identity of the atoms is needed for measuring duration of 
contact. g_dist does something like this, and reading g_mindist -h 
should have prompted you to find this out.

Otherwise, you will have to construct an index group for each water 
molecule, and script a loop to examine each water molecule separately 
using some tool that observes what you really want to measure.

> so for that i need the whole 5ns frames because am looking for water 
> molecules which reside more than 50% of time.

You also need to be clear about whether you care about continuous 
contact. Does a water molecule that oscillates at a distance around the 
cutoff reside about 50% of the time?

You still don't need high time resolution for testing whether this 
analysis might give you the information you want. The water molecules 
that are in contact for more than 50% of the time (continuous or not) 
will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots 
every picosecond is better, but not if you can't afford to wait for it.

Mark

>
> Thanks
>
> On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto: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 <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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>
>
>
> -- 
> Aiswarya  B Pawar
>
> Project Assistant,
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>

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