[gmx-users] help please @User-specified potential functions

[Mark Abraham]

Yes. Three parameters are needed for nbfunc 2 in order to use the few
kernels that implement Buckingham; using a Buckingham-shaped table with
nbfunc 1 is not "using Buckingham" from the point of view of how many
parameters grompp will expect.

Mark
On May 30, 2014 8:19 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:

> Thanks. So let me rephrase so that I get your point:
>
> I reread the document by Gareth. As described in section 2 (changing the
> form of global interaction), nbfunc is set to 1, even if potential is of
> 6-9 form instead of 6-12 form of Lennard Jones. Now, even for buckingham,
> only C and A need to be provided, since B can be clubbed with function of r
> i.e. exp(-B*r), as you mentioned in the beginning of last email of yours
> (although the *source of the confusion was the note 1 on the bottom of page
> 2 of this document*, which says 3 parameters A, B and C need to be provided
> for buckingham). Thus, nbfunc=1 should work even if some pairs interact via
> buckingham while others by LJ.
>
> Please comment.
>
> Thanks
> Chetan
>
>
> On Fri, May 30, 2014 at 12:02 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On May 29, 2014 2:28 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
> > >
> > > Dear All,
> > >
> > > I just came across this fantastic capability of Gromacs, user-specified
> > > potential functions, which can let me use LJ potential for some atom
> > pairs
> > > whereas Buckingham for some others. However, I have a doubt about
> > topology
> > > file construction, even after reading a document by Gareth and going
> > > through earlier posts on this mail-list. I would be highly obliged if
> > > anyone can help:
> > >
> > > Specifically, since I have LJ and buckingham both, do need to repeat
> > > statement mentioning nbfunc ( and combination-rule) in .top file? e.g.
> > > nbfunc=1 followed by LJ parameters  C and A for the concerned pairs and
> > > then nbfunc=2 (and whatever combination rule) , followed by buckingham
> > > parameters C, A , B for concerned pairs in the .top file?
> >
> > Gareth's approach relies on absorbing the extra parameter for Buckingham
> > into h(r) of the table and specifying which tables are used by which
> pairs
> > of atom types. That should work, but IIRC is capped by the allowed number
> > of energy groups, probably 64. My earlier point was that GROMACS can only
> > do the same thing with the parameters for the two interaction types right
> > up to the point the table is used, so you must express in the topology
> the
> > right values for whichever nbfunc value you choose as convenient. You
> can't
> > choose a second value for nbfunc anywhere. Depending on your values and
> > combination rule, you might need to absorb a scaling factor into g(r) or
> > h(r), too!
> >
> > Mark
> >
> > > Thanks a lot!
> > >
> > > regards
> > > Chetan
> > > --
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