[gmx-users] User-define non bonded table

[Steven Neumann]

Thank you.
Another question... I specify in my table functions e.g. g(x) and h(x) and
it is written that I need to setup parameters C6 and C12. But where I
should specify them? In :

[ atomtypes ]
;name at.num mass charge ptype V(c6) W(c12)
O 8 15.99940 0.000 A 0.22617E-02 0.74158E-06

or

[ nonbond_params ]
; i j func V(c6) W(c12)
O O 1 0.22617E-02 0.74158E-06
O OA 1 0.22617E-02 0.13807E-05

Or maybe both?


On Fri, Jun 7, 2013 at 12:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/7/13 7:36 AM, Steven Neumann wrote:
>
>> Thank you, just getting into this. I just dont understand why they start
>> from x=0.04? Why not 0.02 or sth else?
>>
>>
> You can start the table from whatever value of x that you like, but at a
> certain point, it is unlikely that particles ever come that close, given
> normal repulsive potentials.
>
> -Justin
>
>
>  On Fri, Jun 7, 2013 at 11:36 AM, Mohan maruthi sena
>> <maruthi.sena at gmail.com>wrote:
>>
>>    Hi Neumann,
>>>                              You  can use tabulated potential option in
>>> gromacs. Please check the site given below:
>>>   http://www.gromacs.org/**Documentation/How-tos/**Tabulated_Potentials<http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials>
>>>
>>> Thanks,
>>> Mohan
>>>
>>>
>>> On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann <s.neumann08 at gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>>  Dear Gmx Users,
>>>>
>>>> I want to specify a table to mdrun for non bonded parameters. I wish to
>>>>
>>> set
>>>
>>>> it up for all atoms with same potential. Is there any example of the
>>>>
>>> table
>>>
>>>> like this? I want use my specific potential so table should have two
>>>> columns: X distance [nm] and Y Potential energy {kJ/mol]. Is that right?
>>>> How can I tell gromacs to use it for all interactions?
>>>>
>>>> Thanks
>>>>
>>>> Steven
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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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