[gmx-users] bonded interactions in Gromos96

[Ehsan Sadeghi]

Hi gromacs users,

I tried to add new bonded interactions to the ffbonded.itp file in gromos96, but I am confused about the used parameters in the descriptions. Here is an example:

#define gb_1        0.1000  1.5700e+07
; H  -  OA      750   

The equation used in gromos is Vb(r_ij)=(1/4) k_ij (r_ij^2 - b_ij^2)^2

I see two unknowns: k_ij and b_ij; but there are 3 numbers in the definition: 0.1000, 1.5700e+07, 750.


The same story for the angle potential:

#define ga_1         90.00      380.00
; NR(heme)  -  FE  -  C          90


The equation used in gromos is Va(theta_ijk)=(1/2) k_ijk (cos(theta_ijk) - cos(theta0_ijk))^2

I see two unknowns: k_ijk and theta0_ijk; but there are 3 numbers in the definition: 90.00, 380, 90.


I appreciate if somebody could clarify this for me.

Ehsan