Re: Reference for GB model 2

From: Andreas Svrcek-Seiler <>
Date: Thu 17 Oct 2002 22:34:40 +0200 (CEST)

> Dear Amber User,
> I used cutoff=16.0, igb=2. The results fit very well with all of the
> experimental data. I read sometime ago that cutoff in GB is recommended to
> be set as a large value. I guess this is a personal opinion instead of a
> general recommendation to all amber users. Correct me if I am wrong.
... A hard cutoff is generally a bad thing - in principle.
When you use a cutoff in conjunction with GB, you're actually cutting off
two things:
1) The contribution of atom j to the (inverse) effective born radius of
atom i if they are seperated by more than than 'cutoff'.
This is rather harmless, since this contribution drops of with
dist**(-4) and the radii are not too accurate anyway (crudely
speaking, with lots of details omitted).
*But* this cutoff alone still generates discontinuities in the energy

2) The Coulomb (a), 'pairwise solvation' (b) and Van der Waals
anergy and force contributions (c).
This is worse (produces 'larger' discontinuities) for (a) and (b)
although they *tend* to cancel each other (just look at the GB
and Coulomb formulas).
(c) is harmless at 16 A (except for purists, maybe).

I have also seen evidence that a cutoff is not worse than no cutoff
in implicit solvent MD (when comparing 'simulated' and experimental
structures), as long as the heat bath takes care
of the drift induced by the cutoff. However, doing so one relies
on the cancellation and/or masking of individual errors,
which should at least always be kept in mind.
It's probably better to use no cutoff and generate shorter trajectories
(or to buy faster machines :-)

If you like to justify using a cutoff, there's a paper
where Dominy and Brooks investigated that in some depth:

Dominy, B. N. and Brooks, C. L. III

Development of a Generalized Born Model Parameterization for
Proteins and Nucleic Acids

J. Phys. Chem. B

->thats nearly ready to enter a bibtex file.

hope this helps,

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Thu Oct 17 2002 - 13:34:40 PDT
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