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.
/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-- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > -- > ------ > 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/ > ----- > -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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