[gmx-users] problem with trjconv

[Mark Abraham]

> Hi all,
> I am trying to use *trjconv command for -pbc but POPC molecules are
> breaking
> when visualize in VMD. The commands  used are
> grompp -f  pr.mdp  -c  em_out.gro -p .top -n index.ndx -o out.tpr
> trjconv  -f em_out.gro  -s out.tpr  -o trj_out.gro  -pbc inbox or cluster
> or
> whole
> Thi trj_out.gro contain broken POPC molecules

GROMACS doesn't ever write molecules that are broken across periodic
boundaries. Thus either you've introduced a visual artefact with your use
of VMD, or your EM produced a broken molecule through using a broken
physical model. You should examine the nature of "broken", and/or try
using ngmx to confirm what is really going on.

Your grompp-trjconv sequence is not necessary for massaging the PBC
behaviour of your EM output. trjconv will accept a .gro file for the -s
flag, which you will see is indicated in the section of the output of
"trjconv -h" that deals with the -s flag. This is quite general GROMACS
behaviour.

Mark