VMD-L Mailing List

From: Olaf Lenz (olenz_at_fias.uni-frankfurt.de)
Date: Thu Jul 26 2007 - 09:20:03 CDT

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Hi!

sally cii wrote:
> Thank you for your reply. When I loaded the AMBER parm file (which
> should contain box information) and then trajectories into VMD, by
> default VMD draws a rectangular box for that trajectory, can I ask how
> does VMD makes this box? and if I use this rectangular box rather than
> the original truncated octahedral box to wrap the trajectory, how
> would that change the trajectories?

I don't know how the Amber plugin interprets the box information, but I
would expect that it automatically computes the correct periodicity
information, so that you can easily use rectangular boxes or the
parallelepiped, whatever you prefer.
Doing so should not change your trajectory (modulo th wrapping itself,
of course).

Olaf

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