[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

rocwhite168 rocwhite168 at 163.com
Thu Aug 2 21:24:18 CEST 2012

Thanks! Your suggestion 3 solves the problem!

On Wed, Aug 1, 2012 at 2:25 PM, Christopher Neale
<chris.neale at mail.utoronto.ca> wrote:
> 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.

Yes. topol.tpr matches traj.xtc. But indeed trjconv shouldn't need the
structure file and removing -s topol.tpr option eliminates the

> 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.

Usually no. Even in the case that there is such index file, index.ndx
matches the system being analyzed.

> 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).

Yes. I set xtc-grps to contain only part of the system in grompp.mdp
before generating the topol.tpr input file. Generating a new tpr file
will indeed make the analysis tool happy. Thanks!!

However, I think the analysis tools can be made a little more
convenient, since generating a new tpr file means that all conf.gro,
grompp.mdp, and topol.top have to be changed accordingly. This will be
a lot of (meaningless) work -- or am I missing some easier approach



> 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
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