Re: AMBER: about wrap the trajectory

From: Carlos Simmerling <>
Date: Thu, 26 Jul 2007 12:28:33 -0400

if you wrap in ptraj there's really no way to wrap to a rectangular
box- and if you did, some molecules may overlap. you should
wrap back to the same box used in the MD unless you really know
what you're doing (and can go through the extra steps you would need)

On 7/26/07, Rachel <> wrote:
> Dear all,
> I solvated my protein with truncated octahedral water box, and the iwrap is
> set to 0, and I want to image the trajectory back to primary box for
> analysis, can I ask if I used a rectangular box rather than a truncated
> octahedral box to wrap the trajecotries, will that change the trajectories
> or the results would still be the same? thank you.
> Kind regards,
> Rachel
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Received on Sun Jul 29 2007 - 06:07:24 PDT
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