[gmx-users] I have questions for tabulated bonded potentials
jalemkul at vt.edu
Wed Aug 31 02:38:40 CEST 2016
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
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 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
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