[gmx-users] Molecule out of pbc box

[chris.neale at utoronto.ca]

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