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AMBER Archive (2004)Subject: RE: AMBER: Turning off non-bond interactions
From: Chris Moth (chris.moth_at_vanderbilt.edu)
A bit more information perhaps:
My vdw radii diea of course introduces undesired attractive forces... and I
The non-bonded electrostatic interactions are tightly integrated into
In ew_directp.h (included by ew_direct.f) there is this interesting piece of
if ( delr2 .lt. filter_cut2 )then
You _might_ get away with modifying this to something like
if ( delr2 .lt. filter_cut2 .and. delr2 .gt. .00001 )then
but that is risky - given that I don't fully understand the pme
I also looked for a quick way to simply exclude your atoms from all non-bonded
Couple of other ideas: You might also try pmemd from Robert Duke instead of
If explcit solvent is not important, you might try using Generalized Born with
If the problem is localised to just one pair of atoms, you could fudge things
Sorry to not have a better answer. Hope some of the more experienced
Chris Moth
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