Re: [AMBER] Fast ibelly?

From: Ross Walker <>
Date: Tue, 20 Mar 2012 11:31:10 -0700

Hi David,

> What I meant by fast is skipping all the belly-belly interactions, and
> also using an implicit solvent model (then PME issues are bypassed). I
> don't think there is a fundamental reason that belly shouldn't work
> with igb>0 because something similar works in NAMD. NAMD has a feature
> to fix atoms, which allows for a very fast simulation of a fixed
> protein and flexible ligand. Unfortunately, it seems like their

I still think there is an issue. The fact it is in NAMD does not mean that
it is actually implemented formally correctly. It may just work for the
wrong reasons. I would certainly think carefully about the equations,
especially the derivatives to be sue it makes sense before proceeding. Maybe
one of the more GB experts on the list can chime in here.

> implementation of OBC generalized Born doesn't take advantage of fixed
> atoms, as it is only marginally faster than a fully flexible implicit
> solvent simulation. I don't know if it would be easier to accelerate
> the GB implementation in NAMD or belly calculations in AMBER, but AMBER
> has a wider variety of and greater flexibility with implicit solvents,
> including the critical ability to separate cavity and van der Waals
> terms in the nonpolar solvation free energy.

You might want to try NAB. This supports GB and may already have the option
to skip belly belly interactions so may already give you what you want.
Alternatively adding support like this to AMBER's GB code is actually fairly
easy to do assuming one doesn't need to worry about belly-belly GB Radii

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Tue Mar 20 2012 - 12:00:04 PDT
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