[gmx-users] Representing bond coupling function form in a flexible water model

WU Yanbin wuyb02 at gmail.com
Tue Jul 12 05:12:31 CEST 2011

Dear GMXers,

I'm trying to implementing a flexible water model in "Gordillo, M.C.; Marti,
J. *J. Phys.: Condens. Matter* *2010*, *22*, 284111" using GROMACS.

The intra-molecular water potential has the following form:
V=D{[1-exp(-alpha*r1)]^2 + [1-exp(-alpha*r1)]^2} + k_a /2 *r3^2 +
k_a*r3*(r1+r2) + k_rr *r1*r2
where r1, r2 is the O-H bond distance and r3 is the H-H distance.

The first term can be modeled using Morse potential.
The second term can be model by harmonic potential.

Could anyone give some suggestions about how to implement the remaining two
coupling terms in GROMACS? Or can anyone recommend other packages that
support these function forms?

Thank you.

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