[gmx-users] truncated LJ potential

Makoto Yoneya makoto-yoneya at aist.go.jp
Mon Jan 10 15:57:46 CET 2011

Dear David and Hess:

Thanks a lot for quick replies.

>> please look into gromacs' table potential functionality, it is described 
>> in the manual, and you won't have to program anything
>> UNLESS the sigma is different for different atom pairs, in that case I'm 
>> not sure if it will work.

The target system has many different atom types with different sigmas (and
I'd like to switch between the standard LJ potential simulation and the
repulsion only one with the same LJ parameter sets for the real compounds
not simplified models.

> You can make different tables for interactions between groups of atoms
> different sigma's by putting these groups in different energy groups,
> but this might get tedious.

As the modification which I'd like to try is very simple one from the 
original LJ function, I'd like to try to modify the code instead of
many kinds of the tables for each pairs of atom types.

> 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.

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.

Thank you for advance.

Makoto Yoneya, Dr.

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