I am a new student of molecular dynamics. I have started using GROMACS a month ago.

I have a small box of 8192 molecules each with 3 atoms. I froze the last molecule and ran the simulation. I even converted the .trr file from binary to .gro and checked that the last molecule indeed stayed in the same place.

However, I want the .trr file to print the force on each molecule or each atom - in the x, y, and z-direction.
I even set the nstfout in the grompp.mdp file to a reasonable non zero number - 5000.

However, the .trr file - when converted to .gro - did not show the force. Can someone tell me what I am doing wrong and how to get GROMACS to save/reveal the force in the .trr file?

  • $\begingroup$ It may be considered off-topic as the question is about using program - more appropriate on computational science SE $\endgroup$
    – Mithoron
    Nov 30 '15 at 10:29
  • 4
    $\begingroup$ I don't think this is off-topic here. However, it may well be true that other sites may be able to answer better. $\endgroup$
    – Curt F.
    Nov 30 '15 at 12:18
  • 2
    $\begingroup$ The GROMACS Users mailing list is a good place for such questions gromacs.org/Support/Mailing_Lists/GMX-Users_List $\endgroup$
    – mabraham
    Feb 1 '16 at 17:07

Gro output format does not support forces, so using it as an intermediate output format defeats your purpose.


gmx traj -f your.trr -of

which runs the gmx wrapper binary, calling the traj module to do trajectory processing, names your input trajectory file after -f and triggers the output of forces with -of (optionally named after -of, defaulting to force.xvg), or similarly

gmx dump -f your.trr

to dump the entire contents of the file including forces) to the terminal.

See also

gmx help traj


gmx traj -h

or http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-traj.html

Note that I currently develop GROMACS.


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