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.slawo...@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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