Hello all, I have done two independent GROMACS run for same protein system.
I would like to cluster and do further analyses. I used the following commands: 1. g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -f2 md_0_1_noPBC_simulation2.xtc -m rmsd-matrix.xpm Selected '4' for back bone atoms. This passed smoothly. 2. g_cluster -s md_0_1.tpr -f md_0_1_noPBC.xtc -dm rmsd-matrix.xpm -dist rms-distribution.xvg -o clusters.xpm -sz cluster-sizes.xvg -tr cluster-transitions.xpm -ntr cluster-transitions.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.20 -method gromos Selected '4' for back bone atoms. This command gives an error as follows: Selected 4: 'Backbone' Last frame 500 time 1000.000 Allocated 1891080 bytes for frames Read 501 frames from trajectory md_0_1_noPBC.xtc Reading rms distance matrix 100% Converted a 501x501 matrix with 80 levels to reals The RMSD ranges from 0.0605 to 0.222 nm Average RMSD is 0.154099 Number of structures for matrix 501 Energy of the matrix is 25.4992 nm WARNING: rmsd minimum 0 is below lowest rmsd value 0.0605 Back Off! I just backed up rms-distribution.xvg to ./#rms-distribution.xvg.1# Making list of neighbors within cutoff 100% Finding clusters 1 Found 1 clusters Writing middle structure for each cluster to clusters.pdb Back Off! I just backed up clusters.pdb to ./#clusters.pdb.1# Counted 0 transitions in total, max 0 between two specific clusters Back Off! I just backed up cluster-transitions.xpm to ./#cluster-transitions.xpm.1# ------------------------------------------------------- Program g_cluster, VERSION 4.6.3 Source code file: /home/uoh/Downloads/gromacs-4.6.3/src/gmxlib/matio.c, line: 1181 Fatal error: hi (0.000000) <= lo (0.000000) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- What is the solution? Thanks for your time. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.