Re: [AMBER] atom coordinate disagreement with sander TI

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

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.


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Received on Thu Oct 09 2014 - 05:30:01 PDT
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