[gmx-users] output file format under pbc

[Chang Woon Jang]

Dear Grimaces Users,

   When I run a simulation with NPT under periodic boundary condition, the
output file (confout.gro) is obtained with shrinked box due to the external
pressure. Because of the periodic boundary condition, some molecules might
be cross the boundary appearing the other side of box as shown in Figure 1
attached.

Is there a way to reformat the output file as shown in Figure 2? I would
like all molecules to have continuous molecules.

Thank you.

Best regards,
Changowon Jang