[gmx-users] g_msd segmentation fault
Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Cheers Gavin -- gmx-users mailing listgmx-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
Re: [gmx-users] g_msd segmentation fault
On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Running out of memory would be the first suggestion. A segmentation fault is a generic error message when a C program (ie. GROMACS) has assumed that it can get access to a certain amount of memory, but is in fact doing so in a way that breaks the rules that segment memory so that one (part of a) program can't hurt another one. Running in single precision will roughly halve your memory requirements, probably without affecting your results. Reducing the number of frames can help also, but it seems you already have fairly few frames. Using -mol probably increases the amount of memory you need by an amount proportional to the number of such molecules (or maybe its square?). Mark -- gmx-users mailing listgmx-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
Re: [gmx-users] g_msd segmentation fault
On Mon, 2012-03-05 at 23:56 +1100, Mark Abraham wrote: On 5/03/2012 11:39 PM, Gavin Melaugh wrote: Dear All I have a system of 40 solute molecules in 480 crown ether solvent molecules. When I ran the msd analysis on the solvent molecules using the following comand. g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg I get a segmentation fault as follows Select a group: 4 Selected 4: 'SOL' Split group of 16800 atoms into 480 molecules trn version: GMX_trn_file (double precision) Reading frame 800 time 4.000 Segmentation fault However when I perform the same analysis on the solute molecules it runs to completion. I have checked the configuration of the system at frame 800 and everything seems to be fine. I have also analysed the energy and there seems to be no problem. Has anybody any idea of what might be happening? Running out of memory would be the first suggestion. A segmentation fault is a generic error message when a C program (ie. GROMACS) has assumed that it can get access to a certain amount of memory, but is in fact doing so in a way that breaks the rules that segment memory so that one (part of a) program can't hurt another one. Running in single precision will roughly halve your memory requirements, probably without affecting your results. Reducing the number of frames can help also, but it seems you already have fairly few frames. Using -mol probably increases the amount of memory you need by an amount proportional to the number of such molecules (or maybe its square?). Mark However, it seems that the mol flag of g_msd is still buggy as described by: http://redmine.gromacs.org/issues/774 Unfortunately, this bug is still not fixed, though a patch seems to be provided. My workaround for this problem is to convert the trajectory with trjconv using the flag -pbc whole and apply g_msd without the -mol option, but providing appropriate index groups for every single molecule. Unfortunately, this method is very time consuming, because the trajectory has to be read, many many times. Afterwards, I just average the results for the different molecules and derive the diffusion coefficient from the averaged MSD. /Flo -- 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 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-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
