[gmx-users] Fwd: shift the LJ potential

[Wes Barnett]

On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:

> Hi Mark
>
> I have a given function for pseudo hard-sphere potential, which has
> different powers than LJ and a constant. I have to insert the constant in
> order to properly define the cut-off for my hard spheres.
> I just realized that I can use "user-specified potential". I guess I can
> include the constant there, yes?
>
> One more thing, I need to have my own particles, spheres with a diameter
> "a". How can I have them in gromacs?
> .
>

This should get you started in generating your own tables:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials

If all you're looking to do is create repulsive spheres (again, not true
hard spheres as Mark said; just removing attractions from the
interactions), then cut off your interactions at 2^(1/6)*sigma and shift
the potential at the cutoff to zero in your table. If you want different
size spheres you need to subtract an additional term from r in the
denominators of the c6 and c12 terms.

-- 
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu
http://wbarnett.us