[gmx-users] using more processors for g_mindist
aiswarya pawar
aiswarya.pawar at gmail.com
Wed Feb 29 11:05:25 CET 2012
Mark,
In the g_mindist output data gives which atom was within cutoff to protein
atom ie the output file of g_mindist
5.000000e+02 518 42680
5.010000e+02 518 20942
5.020000e+02 518 67844
5.030000e+02 518 5984
5.040000e+02 518 67844
5.050000e+02 518 5984
5.060000e+02 518 30116
5.070000e+02 518 67844
5.080000e+02 518 32957
5.090000e+02 518 67844
5.100000e+02 518 19610
5.110000e+02 518 19610
5.120000e+02 518 22895
5.130000e+02 518 30116
5.140000e+02 518 19610
5.150000e+02 518 22895
5.160000e+02 518 13628
5.170000e+02 518 5984
2nd column is the protein atom and the 3rd column the water atom.
if iam doing g_dist how is it possible to know the which water molecule has
to be considered for the distance calculations ie should i compute the
distance between one protein atom against all the water within the cut off
individually?
Thanks
On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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>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
>>>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
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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
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Aiswarya B Pawar
Project Assistant,
Bioinformatics Dept,
Indian Institute of Science
Bangalore
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