[gmx-users] User-define non bonded table

[Justin Lemkul]

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

>
> 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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-- 
========================================

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

========================================