Hi, On Mon, 25 Sep 2017 14:11 Du, Yu <[email protected]> wrote:
> Dear GMX Users, > > > Indeed making tabulized potential between groups with Verlet is not > trivial as also discussed in OpenMM issue #1765. > > I'm using gmx 2016.3. If I want use the group NS scheme as precise as > possible, what parameters in mdp file should I set and what are their > recommended values for protein and ligand system. > It's straightforward to implement a tabulated interaction kernel, but rather less clear how best to let the user describe to mdrun how they want the calculation to work, eg whether interaction types should be governed by atom numbers, or types, or names, and how that should be expressed in the topology. Suggestions for problem types people want to be able to handle are most welcome. How to set up the nonbonded scheme for a given force field varies with the force field, either based on how it was parameterized or been shown to work in practice. This is standard practice. A major defect of the group scheme is that it is inefficient with a buffered list, but that is your tradeoff to make. Given that you are modifying the force field to add different interactions, you will anyway have to show that the modified form of the force field works suitably. Even if the Verlet scheme had support for tabulated interactions, you would still be limited to having only one set of nonbonded parameters per atom type. Is your mix of interaction types feasible to use with such a restriction? Mark > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
