[gmx-users] truncated LJ potential

Makoto Yoneya makoto-yoneya at aist.go.jp
Tue Jan 11 02:10:56 CET 2011

Dear Berk:

Thanks again for the further reply.

>> The LJ potential and force code in the above looks like in the c6-c12
>> not in epsilon-sigma one.
>> The LJ potential modification I'd like to try is based on the epsilon-
>> sigma form and the mixing rule is the Lorents-Bertelot's one.
>> Could you kindly tell me the LJ potential and force routine in the
>> Sigma form.
>There is no such code.
>You can simply check for rinvsix > c6/c12

Is it means that the LJ potential in epsion-sigma form (with the
mixing rule) is evaluated after the coversion into c6-c12 form in GROMACS?
Then, may I evaluate the modified LJ potential:

> > V(r)
> >    = 4*epsilon*{ (sigma/r)^(12) - (sigma/r)^6 + (1/4) } for r<=
> > 2^(1/6)*sigma
> >    = 0 for r>  2^(1/6)*sigma

with translated into the equivalent c6-c12 form:

   = (c12/r)^(12) - (c6/r)^6 + (c6/2)*(c6/2*c12) for r<= (2*c12/c6)^(1/6)
   = 0 for r > (2*c12/c6)^(1/6)

in the following routines.
> > You can also set the environment variable nb_generic.c and modify
> > src/gmxlib/nonbonded/nb_generic.c, but might lead to somewhat
> > slower simulations.

If my understanding in the above would correct, I'll try that.

Thank you for advance.

Makoto Yoneya, Dr.

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