Deas jason,
Great. Thanks for the explanation.
best regards
setyanto
On Tue, Aug 9, 2011 at 9:56 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> On Mon, Aug 8, 2011 at 10:09 PM, setyanto md <stwahyudi.md.gmail.com>
> wrote:
>
> > Dear Amber User and developer,
> >
> > I read at AMBER 10 Manual, page 37, at the desription of "cut", it is
> said
> > that "For PME, the cutoff is used to limit direct space sum, and the
> > default
> > value of 8.0 is usually a good
> > value. When igb>0, the cutoff is used to truncate nonbonded pairs (on an
> > atom-by-atom basis); here a larger value than the default is generally
> > required."
> >
> > My simulation use explicit solvent mode, so this mean igb=0 by default,
> > according to the manual it is enough using cutoff 8 angstrom.
> >
>
> Typically, yes. You will hear some disagreement about it, but for explicit
> solvent using PME, the cutoff only *really* applies to the VDW
> interactions,
> which decay as 1/r^6.
>
> While it does also limit the direct space sum in PME, the reciprocal space
> sum picks up with the direct space sum doesn't get, so you get the full
> electrostatic interaction. The direct space scales as N^2 and the
> reciprocal space sum scales as N log N, so a smaller cut yields a cheaper
> calculation (to an extent).
>
> For GB, however, the whole electrostatic calculation is a direct sum over
> interacting pairs with no reciprocal space sum to get the rest of the
> interactions. The issue with a small cutoff here is that electrostatic
> interactions decay as 1/r, which is actually a divergent series, so it's a
> very long-range force. As a result, you'll need a much larger (perhaps
> even
> infinite) cutoff to get a decent picture of what's happening.
>
>
> > I want to make sure if this cutoff only related with explicit and
> implicit
> > solvent mode ?
> >
>
> I don't know what you mean here. It's a general nonbonded interaction
> cutoff...
>
>
> >
> > How about th size molecule and number of amino-acid ? is this also need
> to
> > considerate or not ?
> >
>
> Not typically. If the cutoff is significantly smaller than the system
> size,
> then it doesn't really matter how big the system is, you're going to see
> the
> above mentioned effects anyway.
>
>
> > My molecule have 388 amino acid and the size is 53.04 x 55.07 x 58.13 A
> > (volume total is 169792.66)
> >
> > questions:
> > 1. Is this enough to use 8 angstrom as cutoff or need larger cutoff ?
> >
>
> 8 Angstrom cutoff would probably be enough for an explicit solvent
> calculation.
>
>
> > 2. What is the significantly different between 8 and 12 cutoff ?
>
>
> Computational cost, and a *very* little bit of accuracy in the VDW
> calculation. A 12 Å cutoff will be more expensive, since the direct space
> sum is larger.
>
> However, the direct space sum does parallelize better than the reciprocal
> space sum, so you will probably see better scaling (but worse overall
> performance) using a larger cutoff.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Aug 09 2011 - 00:30:02 PDT
