On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi <yunsh...@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). > 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. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
