[gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

Apart from my own simulation, I do no understand how the values of C6 and
C12 are obtained for each atoms in ''atometypes'' in force fields, could
you tell me?


Best regards


On Wed, Oct 11, 2017 at 3:06 PM, Wes Barnett <w.barnett at columbia.edu> wrote:

>
>
> 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
>