[gmx-users] g_msd bug

[Tsjerk Wassenaar]

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