On Wed, May 12, 2010 at 4:11 PM, liu junjun <ljjlp03.gmail.com> wrote:
> Thanks a lot to all of you. Now I understand more. As Bob and Bill pointed
> out, the ele is calculated for those outside the cut when PME is enabled, I
> agree with what Mike mentioned that vdw is quite small at the cut. However,
> in case of vacuum simulation, is there any different algorithms to deal
> with
> the electrostatics that moves out of the cutoff? If there isn't, there
> seems
> to be a convergence problem in vacuum simulation when cut isn't large.
>
I think cut is generally recommended to be infinite in this circumstance (or
large enough to encompass everybody), so the pairlist is complete.
>
> In order to understand this, I made a simple test simulation in vacuum, but
> don't see any problem. I don't know whether the tested simulation indicates
> all nonbond interactions were within the cutoff during the simulated time
> or
> not, so I made another test by fixing the nonbond list.
> 1). set skinnb=0 in the input
> 2). set do_update_list = .false. at the end of check_skin subroutine, so
> that sander stops rebuilding the nonbond list during the whole simulation.
>
> What I found surprises me. The vacuum simulation ran 100 MD steps without
> updating the nblist. The potential energy was going all the way to more
> negative values and the temperature was going all the way to higher values.
> The temperature was 600 K at the 100 step.
>
> Can anybody please explain this?
>
> Thanks!
>
> Junjun
>
> On Wed, May 12, 2010 at 1:11 PM, Robert Duke <rduke.email.unc.edu> wrote:
>
> > 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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> >>
> >>
> >>
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 12 2010 - 13:30:11 PDT
