A simulated tempering dataset of interaction parameters and binding energies

Description

Time series of interaction parameters and corresponding binding energies from a Hamiltonian hopping simulation of molecular binding.

Usage

data(cyclooctanol)

Format

A data frame containing 2 columns and 35000 rows.

Details

The dataset contains ligand-receptor interaction parameters (lambda) and binding energies for the equivalent of an Hamiltonian hopping simulation of cyclooctanol binding to beta-cyclodextrin. (Hamiltonian hopping is the same as simulated tempering except that potential parameters are varied rather than temperature.) This illustrative dataset was constructed by concatenating the output of some of the replicas of a Hamiltonian replica exchange simulation of the same complex (Wickstrom et al. 2013). Harmless discontinuities may be observed at the joining points.

The dataset contains 2 columns and 3500 rows. Rows correspond to consecutive time points. The first column cyclooctanol$V1 contains lambda values (24 discrete values between 0 and 1) and the second column cyclooctanol$V2 records binding energy values in kcal/mol.

References

Wickstrom, L., Gallicchio, E., He, P., and Levy, R.M. (2013) "Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process," Journal of Chemical Theory and Computation, submitted for publication.

Results