Dear all, In the mdp input file of an MD simulation i have: nstxtcout = 20 xtc_grps = cwat I tell mdrun to write the coordinates of a small group of 4 waters to a file called traj1.xtc every 20 steps. the xtc file is created and has a non-zero size. However, if i say:
g_traj -f traj1.xtc -ox cwat1.xvg -s topol1.tpr the group of atoms i want to write is not in the list when g_traj asks me to select a group, although the group is known to the tpr file (as i checked with gmxdump). If i include the index file that contains the group (and which was also used for the grompp command) it is in the list, only if i choose it all the coordinates in the resulting xvg file are zero! If i look at snapshots of the entire system created by trjconv from a trr file of the same run this group of molecules is certainly there and has non-zero coordinates. If I make a new tpr file with the same specifications in the mdp file but with only 4 waters in the input structure and topology, and use this tpr file with g_traj it works and the coordinates are fine. This problem might be due to the fact that I run a parallel job using openmpi (np=4 on a dual processor/dual core machine as in: mpirun -np 4 --hostfile my-hostfile-17 mdrun_mpi -s topol1.tpr \ -np 4 -o traj1.trr -x traj1.xtc -c confout1.gro -e ener1.edr \ -g md1.log >& mpirun1.err & my gromacs version is 3.3.1, on a linux rocs cluster with a recent centos version. a minor issue ... but maybe someone knows how to make it go away ... Michael ____________________________________________________________________________________ Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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