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

[Chang Woon Jang]

Dear Justin Lemkul,

  I got it. Thank you very much for your help.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang <changwoonjang at gmail.com>
wrote:

> 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
>>
>
>
>
> --
>
>