[gmx-users] constant term in dihedral potential function

[Mark Abraham]

Kukol, Andreas wrote:
> Hi,
> 
> I supply the multiple dihedral terms as a combination of single ones, such as:
> 
> ;atom no.              type   phis    k       mult
> 22    23    24    25     1    180    7.470     1
> 22    23    24    25     1    0      3.900     2
> 22    23    24    25     1    180    1.100     3
> 22    23    24    25     1    90    -5.685     0

I don't believe this works in the way you might expect. Page 109 of the 
manual contradicts me, but (undocumented) dihedral type 9 was added 
recently to allow multiple strictly-consecutive dihedrals of type "1" to 
be accumulated on the same atoms. Anyway, this can readily be checked by 
comparing 0-step EM runs, before and after commenting out the last of 
the multiple dihedrals pre-grompp. Also, you can look at a gmxdump of 
the .tpr.

> In case I supply the potential with a Ryckaert-Bellemans dihedral, do I need to exclude the 1-4 interactions between atoms 22 and 25 ?

The form of the dihedral function doesn't matter. See section 5.4 of the 
manual.

> Maybe one Ryckaert-Bellemans dihedral would be also computationally more efficient ?

Maybe.

Mark