hello:
I am using the following command for md production in gromacs:
grompp -f md.mdp -p md.top -o md.tpr
mpirun -np 64 mdrun -s md.tpr -x md.xtc -g md.log
However, I found that the md.xtc file need command:
trjconv -f md.xtc -o convert.xtc -pbc mol
to put the molecule in the centre of pbc box, otherwise it is messy when
we visualize in VMD. I am wondering, is it possible to ask mdrun
generate the .xtc file cetering the molecule in PBC box automatically
and we no longer need to use trjconv command to convert it.
thank you very much
best
Albert
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