[gmx-users] I have questions for tabulated bonded potentials
Chang Woon Jang
changwoonjang at gmail.com
Wed Aug 31 02:35:39 CEST 2016
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
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
> 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 A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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