Re: AMBER: pmemd: same rst, different result?

From: Thomas Cheatham <>
Date: Tue, 18 Dec 2007 23:39:50 -0700 (Mountain Standard Time)

> possible to me to construct a tool that would allow you to do this, but the
> current rub is that ptraj doesn't handle it. SO the basic assertion that you

...actually, ptraj can (I believe) already do this for orthorhombic... I
have yet to generalize this to triclinic (aka truncated octahedron) but
this should be relatively straightforward for those able to penetrate the
code. Everything is peachy (subject to precision) if your particles move
less than 1/2 a box distance between frames processed (i.e. Yong is

Accuracy is a separate issue since unwrapping with finite precision (i.e.
what is stored in the prmtop for box sizes and coordinates) is less
accurate than what is maintained internally in sander/PMEMD. There have
been a few reports that the unwrapping (or equivalently imaging an
IWRAP=0) is less than adequate due to the poor box precision in the
restrt. This is something we hope to address is future releases. In the
meantime, the error is not so severe for diffusion (but could
potentially be for energies or overlap). The key here is the finite
precision of the output files; when unwrapping or wrapping these, the
precision in the box size matters. So, my feeling is that it is better to
do this internally (IWRAP=1) as you recommend...


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Received on Sun Dec 23 2007 - 06:07:02 PST
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