Dear Nimesh:
trjconv -f orig.xtc -s my.tpr -o new.xtc -pbc atom
to get the help information:
trjconv -h
Normally, you might not get an answer to this one since it's the most
commonly asked question. The users list search is, however, not
working right now so I thought I'd pass along the information.
-- original message --
Hi,
Does anyone know if there is a way to put a molecule back in the pbc box in
gromacs. I am visualizing my sims in vmd and the molecule keeps going out of
the box. Is it normal or an artifact in vmd, is there a way to put the
molecule back in the box? please let me know.
Thanks,
Nimesh
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