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 40000.000 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
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