[gmx-users] Shifting in Verlet cut-off schemes?
yunshi09 at gmail.com
Thu Feb 6 17:56:31 CET 2014
On Mon, Mar 4, 2013 at 3:22 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi <yunshi09 at gmail.com> wrote:
> > Hi all,
> > I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but
> > still unsure about how Verlet works.
> > "The group cut-off scheme can be combined with a buffered
> > pair-list......The Verlet list scheme has buffered neighborlists with
> > exact cut-off's". What does "buffered neighborlists" mean? Including
> > neighbors beyond the cutoff distance (e.g. 1.0 nm)? Then what is the
> > delta-distance for this buffer region?
> See manual 7.3.9
> "LJ and Coulomb potential are by default shifted to zero by
> > subtracting the value at the cut-off". Does the program only do such
> > subtractions at exactly the cutoff distance? Or does it shift both
> > potential functions throughout the entire distance range (e.g. from 0
> > to 1.0 nm)?
> The latter. Doing it at the cut-off would serve no purpose at all (since it
> is zero after the cut-off, by definition).
BTW, is this contradicting Dispersion Correction (DispCorr = EnerPres)? Or
is it DispCorr is independent from LJ and Coulomb potential and operates on
> > Then would this cause potential problems since some force fields are
> > not parametrized with a shifting approach?
> In principle, yes. Many force fields were parameterized using methods that
> are either now totally unused, or that remain in favour pretty much because
> of those force fields :-) As always in computational chemistry, you need to
> seek a method reasonably likely to lead to an accurate model of reality.
> Combing the literature for the necessary insight is difficult, but unless
> someone has already done that work for a system similar to yours, you might
> as well be throwing darts at a board as not do it! There will be no
> literature for using the GROMACS 4.6 Verlet kernels, because they're new.
> So there's something of a burden of proof on people adopting it before the
> GROMACS authors publish their thoughts on using it. Work in progress. That
> said, there's no doubting that the Verlet kernels are technically superior
> to the group kernels, in theory and implementation (as discussed on the
> page you linked). The case for using Verlet kernels right now is stronger
> if you don't have much water, want good energy conservation, or anticipate
> a long-term need for strong scaling to lots of hardware. You've no
> alternative if you want to use GPUs.
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