Ah, my prejudices emerge. And as pointed out by Bill and Dave and Mike, pme
does not help with vdw. But the vdw long-range energy term, the dispersion
term, is a function of distance of the form 1 / r**6 - that drops pretty
quickly. So at about 8 angstrom, you are in pretty good shape on vdw
truncation. Some folks will go out to 9 angstrom, and there is a slight
difference; longer cutoffs do have a performance cost though. Darden also
put an analytic correction to the vdw long range calcs in the pme code,
which is routinely used (see vdwmeth). This effects energies and pressures
but not individual atom forces; the correction for atom forces would be
pretty darn small... All this can be played with fairly easily to gain some
sense of the real impact. For PMEMD, you can set the vdw cutoff to really
long lengths if you want without increasing the electrostatic cutoff - you
use vdw_cutoff and es_cutoff in place of cut in the &cntrl namelist, and it
must be true that vdw_cutoff >= es_cutoff. The "skin" is really only a
mechanism to reduce the frequency of pairlist building, since it is an
expensive process; as I think Mike said, using the skin just gives you the
logical equivalent of rebuilding the list at each step (there are various
performance tradeoffs not mentioned...).
Regards - Bob Duke
----- Original Message -----
From: "case" <case.biomaps.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, May 12, 2010 12:57 PM
Subject: Re: [AMBER] skinnb and energy conservation
> On Wed, May 12, 2010, liu junjun wrote:
>>
>> I have a question about how SKINNB works in energy conservation. The
>> nonbond
>> list is extended but vdw and ele interactions truncated at cut. As I
>> understand, the atom pairs in the nblist can be considered as some kind
>> of
>> "candicates" for calculating vdw and ele interactions, and only those
>> with
>> distances less than cutoff are selected to calculate the vdw and ele
>> interactions. If my understanding is correct, then there seems to be a
>> problem in energy conservation. Lets assume there is an atom pair whose
>> initial distance is 9.99A in a system where cut=10A. The nonbond
>> interactions are calculated for this atom pair because 9.99A < 10A. After
>> one MD step, the distance might changes to 10.01A, then the nonbond
>> interactions are not calculated because 10.01 > 10A, which would cause a
>> sudden energy change.
>
> You are correct: the use of skinnb does not remove problems arising from
> discontinuities in the Lennard-Jones terms at the cutoff. Its purpose is
> just
> to reduce the frequency at which the non-bonded pair list needs to be
> constructed.
>
> ....dac
>
>
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Received on Wed May 12 2010 - 10:30:06 PDT
