Dear Gromacs users, I tried to use "g_msd -s topol.tpr -f traj.xtc -o msd.xvg -trestart 500" to calculate the mean-squared displacements. But the results are clearly erroneous: the first 2500 entries in the output are all "-nan", and after that values stat constant (including zeros). I suspected that this may be related to that I have too many frames (20001) and too long simulation length (20 ns), so I tried to reduce them with the command "trjconv -f traj.xtc -s topol.tpr -b 0 -e 1000 -o traj.1ns.xtc" to split the trajectory file, but trjconv exited with an error like "Index[0] 1234 is larger than the number of atoms in the trajectory file (12). There is a mismatch in the contents of your -f, -s and/or -n files."
Now I think both problems may be due to the fact that only a portion of all the atoms in the system have been written to the trajectory, and other atoms are kept fixed. But I am fairly new to Gromacs, and I'm wondering if I have missed anything. Thanks, Roc -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
