# [gmx-users] truncated LJ potential

Berk Hess gmx3 at hotmail.com
Tue Jan 11 11:22:10 CET 2011

```Yes.

The pow function is expensive though. The code will run much faster
if you can use rinvsix, such as check for  2*rinvsix > c6/c12.
(I forgot the factor 2 in my previous mail).

Berk

> From: makoto-yoneya at aist.go.jp
> To: gmx-users at gromacs.org
> Date: Tue, 11 Jan 2011 10:10:56 +0900
> Subject: [gmx-users] truncated LJ potential
>
> Dear Berk:
>
> Thanks again for the further reply.
>
> >> The LJ potential and force code in the above looks like in the c6-c12
> form
> >> 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
> epsilon-
> >> 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
> Lorents-Bertelot
> 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:
>
> V(r)
>    = (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.
>
>
> Makoto Yoneya, Dr.
> http://staff.aist.go.jp/makoto-yoneya/
>
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