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

[Chetan Mahajan]

Hi Mark and Justin,

File written by Gareth Tribello and attached to the end of following page
on GROMACS site discusses how one can specify buckingham interaction for Na
Na and Cl Cl while still specifying Lennard-Jone interaction between Na and
Cl. (page last modified on 9th Feb 2014 by Justin.)

http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s


File by Gareth Tribello mentions example of NaCl, where interaction Na Na
and Cl Cl is buckingham, whereas interaction Na Cl is LJ. But it's not
clear what should one specify nbfunc and comb-rule as, in a .top file.

Also, let me share in the following, paragraph from section 6.9.2 of
Gromacs manual 4.6.5:

"If you want to have different functional forms between different groups of
atoms, this can be set through energy groups. Different tables can be used
for non-bonded interactions between different energy groups pairs through
the .mdp option energygrp-table (see sec. 7.3). Atoms that should interact
with a different potential should be put into different energy groups.
Between group pairs which are not listed in energygrp-table, the normal
user tables will be used. This makes it easy to use a different functional
form between a few types of atoms."

All of this does point out that one can mix LJ and buckingham amongst
different pairs of atoms. e.g. A and B could interact via LJ potential,
whereas A and C (say C is bonded to B) interact via buckingham potential.

Thanks
Chetan


On Thu, May 29, 2014 at 12:51 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I do not think there is any ability in GROMACS to mix LJ and Buckingham.
> Each particle can have only one set of non-bonded parameters, so there is
> no sensible way to express the interaction between the sets of atoms
> natively using each type of interaction.
>
> Mark
> 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?
> >
> > Thanks a lot!
> >
> > regards
> > Chetan
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