[gmx-users] User specified Potential Functions

Tandia, Adama TandiaA at Corning.com
Fri Aug 25 21:37:03 CEST 2006

Dear all:

I would like to use the User specified Potential Function to implement
in Gromacs the modified force field from Winkler et al. [Journal of
Chemical Physics, Vol. 120, No. 1, (2004) pp: 384-393] but I'm not sure
I understand very well how this feature works in Gromacs for LJ type
force fields.
I expect, from Manual Gromacs 3.3 Page 142 (Paragraph 7.3.11 Tables),
one can specify tables with f(r), g(r) and h(r) for every possible pair
of atom types in the system, but the documentation in Gromacs 3.3 does
not say much for Buckingham type force field. Examples in GMXLIB are for
LJ types only.

Does anybody know if the g(r) and h(r) for a Buckingham type force field
will be used in the following way or not?

U(r_ij) = A_ij*Exp[-B_ij*g(r_ij)] - C_ij/[h(r_ij)^6]

With A_ij, B_ij and C_ij read from the topology file.

Warm regards,


Adama Tandia
Modeling & Simulation
Corning INC
SP TD 01-01
Corning NY 14831 USA
Tel:  607 248 1036
Cell: 607 206 3158
Fax: 607 974 3405


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