Hi guys do you have an idea what is causing the segmentation fault with g_cluster?
I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tpr file for the backbone atoms only tpbconv -s run_1.tpr -nsteps -1 -n index.ndx -o topol.tpr 3. I run g_cluster on the combined trajout with the new tpr selecting backbone for RMSD fit and output g_cluster -f trajout_combined.xtc -n index.ndx -s topol.tpr -fit -method gromos -sz clust-size_0.20.xvg -o rmsd-clust_0.20.xpm -g cluster_0.20.log -clid clust-id_0.20.xvg -cl clusters_0.20.pdb -dist rmsd-dist_0.20.xvg -cutoff 0.20 the output is Allocated 12066120 bytes for frames Read 1202 frames from trajectory trajout_combined.xtc Computing 1202x1202 RMS deviation matrix # RMSD calculations left: 0 The RMSD ranges from 0.0601062 to 0.533457 nm Average RMSD is 0.321503 Number of structures for matrix 1202 Energy of the matrix is 160.564 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0601062 Making list of neighbors within cutoff 100% Finding clusters 7 Found 7 clusters Writing middle structure for each cluster to clusters_0.20.pdb Segmentation fault I have tried using less frames (using -dt 500 for trjcat) as to check that it is not a memory issue but still get the seg fault The g_cluster works if I use a trajectory from a single simulations but not for hte combined trajout. I am getting a segmentation fault with both gromacs 4.5.5 (on my macbook pro) and 4.6.3 on raijin.nci.org.au (our supercomputing facilities in Australia) Cheers Evelyne -- View this message in context: http://gromacs.5086.x6.nabble.com/Segmentation-Fault-using-g-cluster-tp4662864p5011006.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
