Hi Dave,
I have a student who has worked carefully on this. I will
send you a NAMD input file, an AMBER input file, and some RNA
coordinates. We can get close to the same energy using PME with a
single point energy calculation. My recollection is that there are
some subtle differences only in electrostatics and VDW because NAMD
uses a smooth switching function for cutoffs.
I will try to send you these today.
Sincerely,
Dave
At 07:51 AM 2/18/2011, you wrote:
>George Giambasu and I are trying to put together a web page giving details of
>what to do to have NAMD use the Amber force fields. But we are having
>troubles getting the level of agreement we would like. Does anyone on the
>list have example inputs they are willing to share that illustrate this task?
>
>...thx...dac
>
>
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___________________________________________________
David Mathews, MD, PhD
Associate Professor of Biochemistry & Biophysics
and of Biostatistics & Computational Biology
University of Rochester Medical Center
Room 3-6830
601 Elmwood Avenue, Box 712
Rochester, New York 14642
http://rna.urmc.rochester.edu
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Received on Fri Feb 18 2011 - 06:00:04 PST
