[gmx-users] output file format under pbc

Chang Woon Jang changwoonjang at gmail.com
Fri Aug 26 05:36:32 CEST 2016

Dear Gromacs Users,

  I would like to describe the situation. An initial molecule in the
periodic boundary condition is located near the right side of box. The box
is big, thus needs to be adjusted and equilibrated under NPT. The box
should be shrinked after few ns seconds. The molecule near the right side
of box during the simulation is moving to the right and some of atoms of
the molecule would appearing the left side of box.

  In this configuration, the molecule looks separated but actually
connected because of PBC. However, I want the molecule as an initial
continuous single molecule in the* "adjusted equilibrated box" *for the
next run. Yes, it is the equilibrated shrinked box.

   Can this be solved by "trjconv" or something else?

Thank you.

Best regards,
Changwoon Jang

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