[gmx-users] Group NS scheme parameter for 2016.3 version

Mark Abraham mark.j.abraham at gmail.com
Tue Sep 26 00:38:55 CEST 2017


On Mon, 25 Sep 2017 14:11 Du, Yu <duyu at sioc.ac.cn> 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?



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