[gmx-users] Fwd: shift the LJ potential

[Mark Abraham]

Hi,

To reproduce the training data for each forcefield, e.g. some experimental
or other computational result, e.g. the density of argon gas under various
conditions. Details of what and how do vary with the force field, are are
documented in its literature, of course.

Mark

On Wed, Oct 11, 2017 at 3:43 PM Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
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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
>>
>
>