[gmx-users] Adding 3 body force field term into Gromacs

Erik Lindahl lindahl at csb.stanford.edu
Wed Jun 2 19:50:29 CEST 2004


This has been covered before on the list, so you might get some more  
info by using the search function at http://www.gromacs.org .

Adding an interaction isn't the problem, but rather how to keep track  
of your interacting atoms. If you have a fixed list of indices that  
interact it is quite easy to implement it as a new bonded interaction.  
If not, the cost of finding all combinations of three atoms close in  
space quickly becomes prohibitive, not to mention that you might need  
several gigabytes of memory just for the neighborlists...



On Jun 2, 2004, at 4:38 PM, Tandia, Adama wrote:

> Dear ALL:
> Has anyone tried to add a tree body term in Gromacs?
> Any functional like Stillinger-Weber (SW) or Axilrod-Teller (AT)?
> SW: e*a*exp(b*(1/(r12/c-d)+1/(r13/c-d)))*(cos(theta)-cos(theta_0))**2
> where e,a,b,c,d,theta_0 are fixed
>  AT:  
> Z_123*[1+cos(theta_123)*cos(theta_231)*cos(theta_312)]/ 
> [r_12*r_13_r_23]^3
> Where Z_123 is fixed
> Thanks a lot,
> Adama
> Adama Tandia
> Modeling & Simulation
> Corning INC
> Corning, NY 14831 USA
> Tel:  607 248 1036
> Fax: 607 974 3405
> www.corning.com
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