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

Mark Abraham mark.j.abraham at gmail.com
Fri May 30 07:02:33 CEST 2014

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!


> Thanks a lot!
> regards
> Chetan
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