> I quote from the Amber 13 manual, page 168 "The current cutoff scheme
> for non-bonded interactions in AMBER modules and NAB does not use a
> switching function to smooth the cutoff."
>
> My question is how does Amber smooth the cutoff?
The manual is correct, Amber does not smooth the cutoff.
PME: With particle mesh Ewald, the full electrostatics are represented.
The cutoff just represents split between the direct space (interactions
within the cutoff) and reciprocal interactions (loosely the longer range).
There is no "cutoff" or discontinuity in the interactions assuming you
properly treat accuracy (determined by the FFT grid spacing, interpolation
order, dsum_tol (error in direct space energy at cutoff) which if using
the defaults are traditionally sufficiently accurate. There is no smooth
cutoff to the van der Waals; it is a hard cutoff. Although one can argue
that other smoothing or switching of forces or energies may be more
accurate, if the cutoff is in the 8-10 A range, the effects are fairly
minimal. For more details, look at work by Steinbach and Brooks. Note that
Amber does automatically apply a "homogeneous density" correction for the
van der Waals cutoff.
GB: With generalized Born, we often recommend using a cutoff larger than
the system size so there are no cutoff discontinuities (and more
importantly, more accurate electrostatics).
More detail is available in various reviews, for example:
Molecular modeling of nucleic acid structure: electrostatics and
solvation. Cheatham TE 3rd, Brooks BR, Kollman PA. Curr Protoc Nucleic
Acid Chem. 2001 Aug;Chapter 7:Unit 7.9. doi: 10.1002/0471142700.nc0709s05.
(noting that a new version of this will be available soon!)
or
T. E. Cheatham, III & B. R. Brooks. ``Recent advances in molecular
dynamics simulation towards realistic representation of biomolecules in
solution". Theor. Chem. Acc. 99, 279-288 (1998).
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Received on Tue Jun 25 2013 - 10:00:03 PDT
