> I disabled imaging for only one residue and now the rdf initial plateau
> looks fine: it dropped from ~0.8 to zero (and the geometry of the curve
> is exactly the same as before, which is encouraging).
>
> By the way you wrote that in this case the problem would be the box size.
Yes, this would suggest to me that either a fix box size is chosen or that
the box is not updating as the trajectory proceeds... [An alternative
explanation is usage of belly or restraints with constant P].
What "overlap" says (please do the checkoverlap with and without imaging)
is that periodic waters are overlapping. This is not possible unless the
waters are not correctly periodic, i.e. if noimage works and image does
not, then there is a problem with the box size. Perhaps you used the box
command to fix the box size?
> Therefore I had assumed that the size of the box should be OK.
Size should be fine. Question relates to whether ptraj has the "correct"
box size at each frame.
--tec3
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Received on Mon Sep 19 2011 - 16:30:03 PDT
