[gmx-users] User-define non bonded table

Justin Lemkul jalemkul at vt.edu
Fri Jun 7 20:09:06 CEST 2013 


On 6/7/13 10:33 AM, Steven Neumann wrote:
> 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.

That may be an erroneous statement.  Within very short distances, you will have 
nearly infinite forces, so zeroes are used instead since these distances should 
never occur.  There's nothing wrong, per se, with entering really huge numbers 
for short distances.

> 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?
>

The table entries must continue until rc + 1 nm, where rc is the longest cutoff 
specified in the .mdp file.

-Justin

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

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

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