RE: AMBER: Turning off non-bond interactions

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Date: Wed, 21 Apr 2004 17:09:26 +0100

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Thanks for taking the time to look into this.
I was using in vacuo simulations intially, sorry for not saying, so the=
 problem isn't with PME specifically.
I'm reluctant to start hacking the core subroutines of sander - as you say=
 I would like a way to turn off non-bonded interactions entirely with some=
 sort of exclusion list, but I don't know if this functionality exists or=
 could be easily added.
I'll try your suggestions of using a tiny radius (and I think epsilon needs=
 to be non zero as well) to prevent atom overlap -- that would probably be=
 good enough for what I'm doing.

Thanks again


---- Message from Chris Moth <> at 2004-04-21=
 10:58:07 ------
>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=20
>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=20
>included in the nonbonded calculations:
> if ( delr2 .lt. filter_cut2 )then
> icount =3D icount + 1
>You _might_ get away with modifying this to something like
> if ( delr2 .lt. filter_cut2 .and. delr2 .gt. .00001 )then
> icount =3D icount + 1
>but that is risky - given that I don't fully understand the pme=20
>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,=
>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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Received on Wed Apr 21 2004 - 17:53:00 PDT
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