On 12/07/2011 1:12 PM, WU Yanbin wrote:
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?
You'd have to write code to do the latter two terms. Consider the
implementation of Urey-Bradley interactions as a template.
Mark
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