Re: [AMBER] atom coordinate disagreement with sander TI

From: Hannes Loeffler <>
Date: Thu, 9 Oct 2014 16:15:30 +0100

On Thu, 9 Oct 2014 07:25:52 -0500
David A Case <> wrote:

> On Thu, Oct 09, 2014, Hannes Loeffler wrote:
> >
> > 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.
> Can you set iwrap=0 and ntxo=2? That avoids wrapping, which will
> almost certainly cause problems in TI, and also removes the size
> restriction on the coordinates in the restart file.

Many thanks. That's a good option.
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Received on Thu Oct 09 2014 - 08:30:03 PDT
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