[gmx-users] problems with some calculated trajectories
Dear users I performed some long-time simulations using gromacs 4.0. The longest simulation trajectory is about 62 ns. Unfortunately the trajectory seems to be damaged. If I calculate the RMSD of different interesting regions the values are beginning to jump up an down after about 17 ns in one case an after about 51ns in another case. At 17802 the RMSD is at 0.23 nm and at the next step (3ps later) the RMSD is at 5.14 nm at 17826 it is normal again (see below). This usually happens only late in the simulation - in a second trajectory this occurs first at about 51 ns. Is it possible that the integration step with 3fs is too big? In other systems it worked fine (also parameterized with the 3 integration step) but there I always stopped the calculation after about 25 ns. Unfortunately I can not visualize these steps in VMD because it simply crashing without giving a reason when trying to load on of the jumping trajectories. Any ideas where the problem is? Gromacs itself never crashed. Are those trajectories lost (a lot of cpu-time was used to calculate them)? cheers Bernhard # This file was created Mon Jun 22 15:37:12 2009 # by the following command: # g_rms -f testSystem.md.trr -s testSystem.md.tpr -o rmsd.TcrCdrs.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 6 [...] @ s0 legend r_208-220 @ s1 legend r_233-244 @ s2 legend r_276-289 @ s3 legend r_320-332 @ s4 legend r_344-357 @ s5 legend r_389-402 [...] 17799.0000.23387230.33084470.28947950.3391822 0.38396970.3377238 17802.0000.20857210.34146160.29597540.3393066 0.39580260.3484098 17805.0005.14690976.19703015.14449214.8545394 4.32179935.2186780 17808.0005.13550816.18953325.13668924.8242044 4.30552585.1988029 17811.0005.10664846.16537955.12447794.8204927 4.30085665.2036052 17814.0005.16283376.17927225.14912564.8215613 4.29667765.2330446 17817.0005.12927396.19008685.13922834.8198600 4.30285985.2275128 17820.0005.18413356.24820855.16944124.8562689 4.33071995.2453709 17823.0005.15871866.21906045.15890884.8293381 4.32159285.2137132 17826.0000.20974200.33797480.28403630.3228907 0.39227180.3273460 [...] ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problems with some calculated trajectories
Hi, Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ? /Erik Bernhard Knapp skrev: Dear users I performed some long-time simulations using gromacs 4.0. The longest simulation trajectory is about 62 ns. Unfortunately the trajectory seems to be damaged. If I calculate the RMSD of different interesting regions the values are beginning to jump up an down after about 17 ns in one case an after about 51ns in another case. At 17802 the RMSD is at 0.23 nm and at the next step (3ps later) the RMSD is at 5.14 nm at 17826 it is normal again (see below). This usually happens only late in the simulation - in a second trajectory this occurs first at about 51 ns. Is it possible that the integration step with 3fs is too big? In other systems it worked fine (also parameterized with the 3 integration step) but there I always stopped the calculation after about 25 ns. Unfortunately I can not visualize these steps in VMD because it simply crashing without giving a reason when trying to load on of the jumping trajectories. Any ideas where the problem is? Gromacs itself never crashed. Are those trajectories lost (a lot of cpu-time was used to calculate them)? cheers Bernhard # This file was created Mon Jun 22 15:37:12 2009 # by the following command: # g_rms -f testSystem.md.trr -s testSystem.md.tpr -o rmsd.TcrCdrs.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 6 [...] @ s0 legend r_208-220 @ s1 legend r_233-244 @ s2 legend r_276-289 @ s3 legend r_320-332 @ s4 legend r_344-357 @ s5 legend r_389-402 [...] 17799.0000.23387230.33084470.28947950.3391822 0.38396970.3377238 17802.0000.20857210.34146160.29597540.3393066 0.39580260.3484098 17805.0005.14690976.19703015.14449214.8545394 4.32179935.2186780 17808.0005.13550816.18953325.13668924.8242044 4.30552585.1988029 17811.0005.10664846.16537955.12447794.8204927 4.30085665.2036052 17814.0005.16283376.17927225.14912564.8215613 4.29667765.2330446 17817.0005.12927396.19008685.13922834.8198600 4.30285985.2275128 17820.0005.18413356.24820855.16944124.8562689 4.33071995.2453709 17823.0005.15871866.21906045.15890884.8293381 4.32159285.2137132 17826.0000.20974200.33797480.28403630.3228907 0.39227180.3273460 [...] ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problems with some calculated trajectories
Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. Reasons for damaged trajectories, even when gromacs runs through fine... ... for me - filesystem issues were causing this. In particular this happened for me with NFS shares and on Lustre filesystems. My NFS problems got solved with an upgrade of the NFS packages on our machines (at least 1 1/2 yrs ago). Best Martin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] problems with some calculated trajectories
Am 22.06.2009 um 17:19 schrieb Martin Höfling: Hey Bernhard, here some thoughts of mine: In principle, vmd should be able to read the trajectories if pdb2gmx tells you that the trajectory is ok. If this is not the case, you can use gmx_rescue64 to extract the undamaged parts. ^ ^^ = gmxcheck :-) Best Martin___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
