[gmx-users] PBC after energy minimization

John Whittaker johnwhittake at zedat.fu-berlin.de
Fri May 1 15:29:26 CEST 2020

Hi Mohamed,

> Hello everybody,
> In order to solve the PBC at the end I use the command:
> *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
> followed by:
> *gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*
> I want to solve this problem after the energy minimization but I don't
> have
> .xtc file to use it as I do at the end.
> How can I solve this problem after the energy minimization ?

You're saying that your energy minimization does not produce a trajectory
(a .trr or .xtc file)?

If that's the case, you just have to instruct GROMACS to periodically
write to a trajectory file using options in the .mdp file (namely,
nstxout). Take a look at:


Under the section "output control" you will find what you are looking for.

- John

> Thanks,
> Mohamed
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John Whittaker
Ph.D. Candidate
Department of Mathematics and Computer Science
Freie Universität Berlin

+49 0160 936 04221

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