RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on"

From: Ross Walker <>
Date: Tue, 31 May 2005 09:09:20 -0700

Dear Grzegorz

> During a short MD I ran using Amber 8 (and Amber 6), water
> molecules did
> not stay inside the box. This is something I didn't encounter using

I'm not quite sure I understand exactly what you are saying here but I think
you are refering to the fact that you see water molecules leaving the
central box during a periodic boundary simulation. This is not a problem,
Amber simply keeps track of the original image so although it looks like it
leaves the central box it's image fills it from the otherside so the
calculation is not affected.

You can check things are okay by using ptraj to re-image the coordinate file
and place everything back into the original box.


For an example of how to do the re-imaging.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue May 31 2005 - 17:53:00 PDT
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