Dommert Florian wrote:
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
It sounds like it's time to file one or more redmine issues for g_msd. Memory
usage might be separate from the inconsistency in the results with or without -mol.
-Justin
/Flo
On Thu, 2011-07-07 at 09:28 +0200, Ivan Gladich wrote:
Dear all,
I found the same problem that Sławomir pointed out 10 days ago about
the memory usage in the computation of g_msd.
I have 100 ns simulation for 2880 water molecules. The trajectory is
savede every 1 ps: this means that I have 100000 frame
I think that there is a strange memory problem only when the option -mol
is used
Indeed, if I use
g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b
4000 -e 100000 -beginfit 5000 -endfit 25000 -trestart 20 -type x
the g_msd does not have any problem
by the way using the option -mol (as Sławomir did in the last e-mails)
g_msd_d -f ../t230.xtc -s ../t230.tpr -n index.ndx -o msdt230.xvg -b
4000 -e 100000 -beginfit 5000 -endfit 25000 -trestart 20 -type x -mol
g_msd crashes and memory information (see below) points out that this
crash is due by the memory overflow.
Thanks a lot
Ivan
Tasks: 478 total, 5 running, 473 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.0%us, 0.5%sy, 12.7%ni, 77.7%id, 9.1%wa, 0.0%hi, 0.0%si,
0.0%st
Mem: 65459256k total, 65382420k used, 76836k free, 0k buffers
Swap: 32009508k total, 5360348k used, 26649160k free, 6312k cached
On 06/27/11 15:40, Tsjerk Wassenaar wrote:
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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--
------
Ivan Gladich, Ph.D.
Postdoctoral Fellow
Academy of Sciences of the Czech Republic
Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.
Flemingovo nám. 2.
166 10 Praha 6
Czech Republic
Tel: +420775504164
e-mail: ivan.glad...@uochb.cas.cz
web page:http://www.molecular.cz/~gladich/
-----
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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