[gmx-users] small questions on tabulated functions

[Chetan Mahajan]

Dear All,

Now I do understand the answer to Q 3 in the earlier email that explicit
cross terms will overwrite mixing rule , after reading through the part of
document, missed earlier. Please advise on Q 1 and 2 in the
earlier/following email.

Thank you very much.

regards
Chetan


On Tue, May 27, 2014 at 3:58 AM, Chetan Mahajan <chetanvm10 at gmail.com>wrote:

> 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
> help:
>
> 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?
>
> Besides,
>
> 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!
>
> regards
> Chetan
>