[gmx-users] User-define non bonded table

Fri Jun 7 16:33:22 CEST 2013

It is stated in manual that tables must always contain 7 columns with a
meaningful data (i.e. no zeros). must be entered in all columns.
The example of table6-12.xvg involves xeros until 0.04. How come?
I want to cut my potential at some point to zero - can I put zeros or shall
I specify some values so the potential will equal zero?

On Fri, Jun 7, 2013 at 2:17 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
>
> 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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