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
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