AMBER Archive (2003)

Subject: Re: AMBER: problems with periodic boundary conditions

From: Michael Crowley (crowley_at_scripps.edu)
Date: Fri Sep 05 2003 - 09:32:29 CDT

Dear Monika,

The older versions of AMBER would "wrap" molecules back into the
primary cell before output and your output would look nice".
However, with that output, one could not analyze trajectory data for
transport properties like diffusion. In later versions, in particular
AMBER 7, we do not wrap molecules back into the primary cell unless
the user specifies iwrap=1 (see docs) in the input. The simulation is
correct even though one observes molecules moving out of the box
and the density appears to be decreasing at the faces. All bonded
interactions are the same, and all nonbonded interactions are still
calculated between nearest images (essentially wrapped back into the
primary cell for nonbond calcs).

Our approach is that the trajectory should be the raw MD output so
that as much analysis can be done as possible. It is not inntended that
researchers should visualize the raw data. The output can be wrapped back
into the cell without changing the raw data using ptraj with the
"image" command to produce a "pretty" output for visualization.

Sincerely,
Mike

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Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail: crowley_at_scripps.edu
Telephone: 858/784-9290
Fax: 858/784-8688
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