From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Thu Sep 02 2010 - 13:30:57 CDT
NAMD determines 1-4 interactions based on the covalent bonds defined in the PSF, not the dihedrals (or impropers). On startup, NAMD searches for the 1-2, 1-3, and 1-4 interactions by following a chain of 1, 2, and 3 covalent bonds, respectively, from each atom. So a 1-4 pair may or may not form the endpoints of a dihedral.
On Sep 2, 2010, at 1:12 PM, Jianhui Tian wrote:
> Dear NAMD users,
> I am trying to understand how NAMD generate 1-4 pairs for the energy calculation. I see many discussion about 1-4 scaling treatment. But first, how does NAMD generate the 1-4 pairs? Does it count all possible 1-4 pairs? Can 1-4 pairs be generated from the dihedral list if I am using psf structure file? Thanks a lot.
-- David J. Hardy, Ph.D. Theoretical and Computational Biophysics Beckman Institute, University of Illinois dhardy_at_ks.uiuc.edu http://www.ks.uiuc.edu/~dhardy/
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