AMBER Archive (2002)

Subject: period boundary

From: Shunzhou Wan (s.wan_at_qmul.ac.uk)
Date: Fri Oct 11 2002 - 10:50:39 CDT

Dear Amber users,

I try to analyze the trajectories using ptraj/carnal. The trajectories
are obtained using other code and converted to amber format. The
coordinates written to the trajectory files were "wrapped" into a
primary box based on atom. That is, for each atom (not molecule), the
image closest to the middle of the "primary box" were the one written to
the output file. In some files, the solute is not visual bonded together
because of periodic boundary. I need to image the trajectory to bring
the molecule back together before further analysis. How can I do to bond
the molecule together?

btw, does amber wraps the coordinate based on molecule? Or atoms in one
molecule bond visual together in output file?

Thanks in advance,

Regards,
Shunzhou