Dear gmx users, I've found a strange problem in g_anaeig. I'm trying to project the trajectory into few first eigenvectors. For this I first do:
g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit -ref -pbc -tu ns Chosing CA group for matrix construction. Then I pick the resulting file eigenvec.trr and do: g_anaeig -v eigenvec.trr -f md_all.xtc -s md0.tpr -filt -n index.ndx -first 1 -last 10 Everything works fine and the output file filtered.xtc should contain nice filtered trajectory. Ok, let's test: g_covar -f filtered.xtc -s md0.tpr -n index.ndx -fit -ref -pbc -tu ns ... ... ... Calculating the average structure ... Reading frame 0 time 0.000 ------------------------------------------------------- Program g_covar, VERSION 3.3.1 Source code file: mshift.c, line: 118 Fatal error: Molecule in topology has atom numbers below and above natoms (238). You are probably trying to use a trajectory which does not match the first 238 atoms of the run input file. You can make a matching run input file with tpbconv. ------------------------------------------------------- What is wrong? It should be the same trajectory as initial md_all.xtc but with different numbers. Any ideas? __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
