Thank you very much for the prompt and comprehensive reply.
Regards
George
On Jun 25, 2013, at 1:31 PM, tec3.utah.edu wrote:
>> 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 - 10:00:04 PDT
