[gmx-users] output file format under pbc

Chang Woon Jang changwoonjang at gmail.com
Fri Aug 26 03:41:06 CEST 2016

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

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

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