Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms?

From: Yong Duan <>
Date: Thu, 08 Dec 2011 14:48:40 -0800

Sorry to interrupt this wonderful exchange :).

As I recall, PME was developed in early 90's by Tom Darden. I don't quite
know why he decided to rebuild the exclusion list but I speculate some
historical events might have justified the move. One thing that we might
have forgotten was the fact that he initially wrote the code as a
completely separate module that relies on or interfaces with the existing
code as little as possible since at the time the main AMBER code
development effort was still at UCSF. As I recall, in the first version
when PME was "experimental", (AMBER 4.0?), the interface between PME code
and the rest was pretty much limited to one line "call ewald_force()".
This way, the code could be developed on its own and can also be easily
ported to other packages, like CHARMM.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/8/11 9:48 AM, "Marc van der Kamp" <> wrote:
>Hi Ross,
>Thanks for your very useful comments.
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Received on Thu Dec 08 2011 - 15:00:03 PST
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