[gmx-users] Fwd: shift the LJ potential

[Faezeh Pousaneh]

I see, thanks Mark,


Best regards


On Wed, Oct 11, 2017 at 3:46 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
>>>
>>
>>