[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
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.
Thank you for advance.
Makoto Yoneya, Dr.
http://staff.aist.go.jp/makoto-yoneya/
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