[AMBER] atom coordinate disagreement with sander TI

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Thu, 9 Oct 2014 12:15:27 +0100


sander(14) claims in some of my simulations that the common atoms do not
have the same coordinates. As these are the final coordinates of a
simulation I had a closer look and found that one state got imaged while
the other one was on the other side of the box (distance between common
atoms exactly the same lengths as one of the box dimensions). Maybe the
code doesn't make sure that imaging is done in sync? I should probably
add that I am running tests on small molecules and traversing of
periodic boundaries is thus quite frequent.

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Received on Thu Oct 09 2014 - 04:30:02 PDT
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