[gmx-users] g_msd bug

[Mark Abraham]

On 27/06/2011 11:57 PM, Sławomir Stachura wrote:
> Hello,
> thank you for your reply. I have used following command :
>
> g_msd  -n POPC.ndx  -lateral z -o POPC_msd.xvg -mol POPC_diff.xvg
>
> Trajectory has 10000 frames and the system it was ran on is Fedora Red Hat 5.4.
> Indeed my network administrator was very unhappy about comsumed memory.

I'd guess that using only part of your trajectory at one time (g_msd -b 
-e, or pre-condition with trjconv) will lead to less memory usage - 
although the implementation of this code should not require 600GB unless 
you actually have many millions of atoms.

Mark

> Regards,
>     Slawomir
>
>
>
>
>
> Wiadomość napisana przez Tsjerk Wassenaar w dniu 2011-06-27, o godz. 15:40:
>
>> Hi Slawomir,
>>
>> That's quite a usage of memory! Can you provide more information? Like
>> the number of frames in the trajectory, the command line you used, and
>> the system you ran on?
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2011/6/27 Sławomir Stachura<stachura.slawomir at gmail.com>:
>>> Hi GMX Users,
>>> I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 bears a problem. I was calculating the MSD od center of mass of POPC in membrane (system contains 274 POPC lipid molecules in all-atom force field) from 50 ns trajectory and it seems to consume great amount of memory. With  time of calculations the memory reserves are gradually devoured to the extent, in my case,  of over 600 GB (than my administrator of cluster killed the process). It seems that it does not release memory and it's pilling results up with steps  in memory. Have you heard of such case?
>>> Best wishes,
>>>    Slawomir--
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>>
>>
>> -- 
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
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