[gmx-users] problems when using trjconv or g_msd to process xtc trajectory files with only a portion of all the atoms in the system

[Christopher Neale]

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