[gmx-users] I have questions for tabulated bonded potentials

[Chang Woon Jang]

Dear Justin,


   Do you mean "Order of parameters"? If I would like to specify for
table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
table_b2.xvg, I need to set 2 after 8.

Am I right?

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang <changwoonjang at gmail.com>
wrote:

> Dear Justin Lemkul,
>
>     I have seen the 4.2.12 and Table 5.5. However, it does not show the
> specific example for several tabulated potentials in topol.top file. I
> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
> table_a2.xvg ... table_a6.xvg, table_d1.xvg .... table_d4.xvg. Those are
> different n values for each interactions.
>
> However, 4.2.12 just says that "Multiple tables can be supplied simply by
> using different values of n, and are applied to the appropriate bonds, as
> specified in the topology (Table 5.5)".
>
> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
> no explanation for distingushing several tables to specify different bonded
> interactions.
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>
>>> Dear Gromacs Users,
>>>
>>>       From the above question, I think that I need to specify the each
>>> bonded interaction in topol.top file. Am I right?
>>>
>>>    For example,
>>>
>>>
>>> [ bond ]
>>> 1  1  2  table_b1.xvg
>>> 2  2  3  table_b2.xvg
>>> 3  3  4  table_b3.xvg
>>>
>>>
>>> Is this right format if I have several tabulated potential files in
>>> topol.top?
>>>
>>>
>> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
>> whether you need to generate exclusions) and the table number is supplied
>> as one of the parameters.  See also section 4.2.14.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>
>
> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj395 at drexel.edu
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj395 at drexel.edu