AMBER Archive (2004)

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

From: Chris Moth (
Date: Wed Apr 21 2004 - 10:58:07 CDT

A bit more information perhaps:

My vdw radii diea of course introduces undesired attractive forces... and I
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 way
to modify the PME implementation to outright ignore atom centers.

In ew_directp.h (included by ew_direct.f) there is this interesting piece of
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 non-bonded
lists... but I did not find it and am out of time. That would be cleaner, I

Couple of other ideas: You might also try pmemd from Robert Duke instead of
sander. Perhaps it can better cope with the overlapping zero valued charges.

If explcit solvent is not important, you might try using Generalized Born with
sander. Then, the pme module is not called at all.

If the problem is localised to just one pair of atoms, you could fudge things
- and introduce a very small partial charge repulsion prior to the collision.

Sorry to not have a better answer. Hope some of the more experienced
folks can help you out.

Chris Moth

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