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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jul 12 05:27:07 CEST 2011

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.

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