[gmx-users] PBC after energy minimization

[John Whittaker]

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:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html

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