[gmx-users] Visualization of conf.gro and confout.gro

[Chang Woon Jang]

Dear Gromacs Users,

   I did NPT simulations with a system containing 15000 atoms of polymers.

Initially, conf.gro was visualized in VMD and showed all connections are
OK. However, the confout.gro (final output configuration) seems to look
bad. Some of bonds are disconnected at the outer surface which I guess the
boundary of simulation box. I think that this is due to the periodic
boundary conditions.

The question is,

If I use the correct topology files, does the confout.gro file can be used
for the further simulation no matter how the visualization look like?

Thank you.

Best regards,
Changwoon Jang,