# [gmx-users] User-define non bonded table

Steven Neumann s.neumann08 at gmail.com
Fri Jun 7 15:17:20 CEST 2013

```On Fri, Jun 7, 2013 at 1:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/7/13 8:21 AM, Steven Neumann wrote:
>
>> 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?
>>
>>
> Try the tutorial first and make sure you can replicate it.  If you're just
> looking to tweak C6 and C12 parameters, there's no need for tabulated
> functions at all.
>
> -Justin
>

I want to change function g(x) to use Chandler Anderson potential so g(x) =
1/r^6 + 1/4sigma^6. Would that be a combination rule 1 with nonbonded
function type 1 in [ defaults ] ? Then in ffnonbonded.itp in [atomtypes]
can I specify my my own C6 C12 ?

>
>
>> 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>
>>>>> <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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ==============================****==========
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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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```