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

Du, Yu duyu at sioc.ac.cn
Tue Sep 26 04:01:46 CEST 2017

> -----Original Messages-----
> From: "Mark Abraham" <mark.j.abraham at gmail.com>
> Sent Time: 2017-09-26 06:38:40 (Tuesday)
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>, "Discussion list for GROMACS users" <gromacs.org_gmx-users at maillist.sys.kth.se>
> Cc: 
> Subject: Re: [gmx-users] Group NS scheme parameter for 2016.3 version
> Hi,
> 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.

I want to decompose the interaction between protein and ligand, and only between them, not others.
So I think "vdwtype=user, energygrps = Protein Ligand, energygrp-table = Protein Ligand and table.xvg table_Protein_ligand.xvg" is the only solution in gromacs to achieve it.

> 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.

Yes, this is my major confusion. Amber FF don't use charge group not like GROMOS FF. I need to work with Amber FF, so is it proper to use amber99sb-ildn and gaff with group cut-off scheme?

And now the manual and user guide is dominated by Verlet cut-off scheme, where can I find the guide of using group cut-off scheme? I can't tell which options is for group scheme in the Molecular dynamics parameters (.mdp).

The following is what I found in regressiontests-2016.3/kernel/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4/grompp.mdp
; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs)
cutoff-scheme            = Group
; nblist update frequency
nstlist                  = 1
; ns algorithm (simple or grid)
ns-type                  = Grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = xyz
periodic-molecules       = no
; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-drift      = 0.005
; nblist cut-off
rlist                    = 0.99
nstcalclr                = -1

Although it use group cut-off scheme, there is also a verlet-buffer-drift, which doesn't show in the 2016.3 version .mdp option.

So, lots of thanks for anyone's advice for setting group scheme.

> 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?

I'm really looking forward to the combination of Verlet cut-off scheme with the tabulated potential. :)

> Mark
> >
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