[gmx-users] Fwd: shift the LJ potential

[Wes Barnett]

On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
wrote:

> Thank you Wes and Mark,
>
> Wes, that is what I am trying to do. However, still have problem.
> I do not know how to derive sigma, epsilon (or C6 and C12) for my particle?
> How the force fields have obtained C6 and C12 values in their .itp files
> for each atom?
>

That depends on what the purpose of your simulation is. If you're just
wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units
could be reasonable.


>
>
> Best regards
>
>
> On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barnett at columbia.edu>
> wrote:
>
>> 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
>> --
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>
>


-- 
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