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

[Justin Lemkul]

On 8/30/16 8:35 PM, Chang Woon Jang 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.
>

In section 4.2.14:

"For each interaction, the force constant k and the table number n are specified 
in the topology."

In Table 5.5 (in the column "Order of parameters and their units"):

table number (≥ 0); k (kJ mol−1)

So for table_b1.xvg with k = 1000 (just an example) to be applied to atoms 1 and 2:

[ bonds ]
; ai aj func table k
   1   2   8   1    1000

-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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