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

Berk Hess gmx3 at hotmail.com
Tue Sep 15 18:11:47 CEST 2009

> Date: Wed, 16 Sep 2009 01:58:02 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] question about using new potential in groamcs
> 青 叶 wrote:
> > 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.
> GROMACS allows the user to supply a tabulated function in r for either 
> bonded or non-bonded interactions. See the manual for details and 
> $GMXLIB/gromacs/top/*xvg for examples here. Assuming you can cast the 
> ion-O interaction and the ion-H interaction in the same functional form 
> your problem might be simple. At worst, you might need to look up 
> different tables for ion-O and ion-H interactions, and this would 
> probably need a code modification.
> Mark

No, you don't need code modification.
There are two ways around this.

1) Put O and H in different energy groups, then you can supply different tables,
but you will loose the water optimization (slower simulations).

2) Use C6=1, C12=0 for ion-O and C6=0,C12=1 for ion-H
then you can fill the dispersion table with the ion-O interaction and the repulsion
table with the ion-H interaction.


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