AMBER Archive (2004)

Subject: Re: AMBER: Turning off non-bond interactions

From: Robert Duke (
Date: Wed Apr 21 2004 - 11:12:11 CDT

Chris -
PMEMD will probably have the same sort of problems; it evaluates direct and
reciprocal forces basically the same way as sander, otherwise I wouldn't get
the same results. Darden probably has the best idea what can and cannot be
done in regards to charges and vdw parameters, having dinked with various
charge catastrophe issues on multipoles.
Regards - Bob
----- Original Message -----
From: "Chris Moth" <>
To: "amber" <>; <>
Sent: Wednesday, April 21, 2004 11:58 AM
Subject: RE: AMBER: Turning off non-bond interactions

> A bit more information perhaps:
> My vdw radii diea of course introduces undesired attractive forces... and
> now have access to our sander source code...
> The non-bonded electrostatic interactions are tightly integrated into
> sander's pme implementation. I have found several 1.0/Rij^2 type terms
> in sander, but, not being a PME guru :), I don't see any quick and dirty
> to modify the PME implementation to outright ignore atom centers.
> In ew_directp.h (included by ew_direct.f) there is this interesting piece
> code - which I believe causes interactions outside the cutoff to be not
> included in the nonbonded calculations:
> if ( delr2 .lt. filter_cut2 )then
> icount = icount + 1
> You _might_ get away with modifying this to something like
> if ( delr2 .lt. filter_cut2 .and. delr2 .gt. .00001 )then
> icount = icount + 1
> but that is risky - given that I don't fully understand the pme
> implementation, and so it might have further unanticipated impacts.
> I also looked for a quick way to simply exclude your atoms from all
> lists... but I did not find it and am out of time. That would be cleaner,
> suspect.
> Couple of other ideas: You might also try pmemd from Robert Duke instead
> sander. Perhaps it can better cope with the overlapping zero valued
> If explcit solvent is not important, you might try using Generalized Born
> sander. Then, the pme module is not called at all.
> If the problem is localised to just one pair of atoms, you could fudge
> - and introduce a very small partial charge repulsion prior to the
> Sorry to not have a better answer. Hope some of the more experienced
> folks can help you out.
> Chris Moth
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