cyclooctanol: A simulated tempering dataset of interaction parameters and...
In UWHAM: Unbinned Weighted Histogram Analysis Method (UWHAM)
cyclooctanol R Documentation
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.
UWHAM documentation built on May 20, 2022, 5:05 p.m.
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| cyclooctanol | R Documentation |
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.
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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