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

[Chang Woon Jang]

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