[gmx-users] g_msd bug

Ivan Gladich ivan.gladich at marge.uochb.cas.cz
Thu Jul 7 09:28:43 CEST 2011

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

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,  
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.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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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.gladich at uochb.cas.cz
web page:http://www.molecular.cz/~gladich/

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