[gmx-users] PBC after energy minimization
johnwhittake at zedat.fu-berlin.de
Fri May 1 15:29:26 CEST 2020
> 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
> .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.
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