[gmx-users] small questions on tabulated functions

Chetan Mahajan chetanvm10 at gmail.com
Tue May 27 11:01:41 CEST 2014

Dear All,

I just came across this fantastic capability of Gromacs, Tabulated
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

1) Specifically, since I have LJ and buckingham both, do need to repeat
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 , followed by
buckingham parameters C, A , B for concerned pairs in the .top file?


2) I guess the order of parameters for Buckingham potential in .top file
would be C, A and B (for the expression in section 4.1.2 and page 69 of the
manual-4.6.5).  Please comment if not so.

3) Is there a way to turn off selection of combination rule totally? This
is since I have all the cross terms for LJ as well as buckingham pairs
myself (it's not advisable to allow direct combination rule, since e.g.
atom X interacts with Y using buckingham, while same atom X interacts with
Z using LJ). I hope there cross terms overwrite comb-rule selection, in
which case, comb-rule specification does not matter.

Thanks in advance!


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