[gmx-users] question about using new potential in groamcs

青 叶 yeqing_121 at yahoo.com.cn
Tue Sep 15 15:46:05 CEST 2009

Hello everybody:
       I have read GROMACS' manual and found that the non-bond interaction in GROAMCS is describled as Coulomb term add A/r^12 -B/r^6 which is named Lennard-Jones term, but recently I have read some papers which use a effective-two-body potential to describle the non-bond interaction in the GROAMCS MD simulation, and this potential works much better in dealing with transition metal ion-water system, in this potential, non-bond interaction between ion and O atom in water molecular is describled as follow:
      V(r)=A/r^4+B/r^6+C/r^8+D/r^12+E*exp(-F*r)+coulomb term; 
where the A,B,C,D,E and F are parameters which can be obtained by fitting the potential energy surface calculated from Ab initio method. r is the distance between the ion and O atom in water molecular, the interaction between the ion and H atom in water molecular has the similar form.
       So my question is how to modify the GROAMCS in order to simulate dynamic course by using this new potential instead of the default L-J interaction. I have tried to find the solution in internet, but so far I still have no idea on this problem, can anybody help me on this problem, I will be very, very grateful for your help.
       My English is not good, please forgive my awkward expression. 
       Best Wishes!
                                                                                                                                Ye Qing

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