1. does topol.tpr really correspond to traj.xtc? You don't need to specify -s to simply use the -b and -e options to trjconv so simply eliminate that.
2. is there a file called index.ndx in that directory? That is the default name of the index file for trjconv input and make_ndx output, so perhaps trjconv is picking up an index file that is not appropriate for this system. 3. You say that only a portion of the atoms have been written to the .xtc. Do you mean that you did that straight out of mdrun? Your trjconv should then work fine if you simply don't give it the .tpr file. To do analysis, you will need to create a new .tpr file that has atoms corresponding to the ones that you wrote out. If, for example, you did not write out the coordinates of one protein molecule, then make a new .top and .gro file corresponding to that system and run them through grompp to get a new .tpr file. You can use this .tpr file for your analysis (but not for simulations of the entire system). Chris. -- original message -- 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
