9
$\begingroup$

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?

$\endgroup$
3
  • $\begingroup$ 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
6
$\begingroup$

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

Use

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

or

gmx traj -h

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

Note that I currently develop GROMACS.

$\endgroup$
0

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.