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dc.contributor.author
Linker, Stephanie M.
dc.contributor.author
Weiss, Richard Gregor
dc.contributor.author
Riniker, Sereina
dc.date.accessioned
2020-12-22T13:35:56Z
dc.date.available
2020-12-21T10:00:00Z
dc.date.available
2020-12-22T13:35:56Z
dc.date.issued
2020-12-21
dc.identifier.issn
0021-9606
dc.identifier.issn
1089-7690
dc.identifier.other
10.1063/5.0019687
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/457683
dc.identifier.doi
10.3929/ethz-b-000457683
dc.description.abstract
Thermally driven processes of molecular systems include transitions of energy barriers on the microsecond timescales and higher. Sufficient sampling of such processes with molecular dynamics simulations is challenging and often requires accelerating slow transitions using external biasing potentials. Different dynamic reweighting algorithms have been proposed in the past few years to recover the unbiased kinetics from biased systems. However, it remains an open question if and how these dynamic reweighting approaches are connected. In this work, we establish the link between the two main reweighting types, i.e., path-based and energy-based reweighting. We derive a path-based correction factor for the energy-based dynamic histogram analysis method, thus connecting the previously separate reweighting types. We show that the correction factor can be used to combine the advantages of path-based and energy-based reweighting algorithms: it is integrator independent, more robust, and at the same time able to reweight time-dependent biases. We can furthermore demonstrate the relationship between two independently derived path-based reweighting algorithms. Our theoretical findings are verified on a one-dimensional four-well system. By connecting different dynamic reweighting algorithms, this work helps to clarify the strengths and limitations of the different methods and enables a more robust usage of the combined types.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
American Institute of Physics
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.title
Connecting dynamic reweighting Algorithms: Derivation of the dynamic reweighting family tree
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
dc.date.published
2020-12-17
ethz.journal.title
The Journal of Chemical Physics
ethz.journal.volume
153
en_US
ethz.journal.issue
23
en_US
ethz.journal.abbreviated
J. Chem. Phys.
ethz.pages.start
234106
en_US
ethz.size
15 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.grant
Passive Membrane-Permeability Prediction for Peptides and Peptidomimetics Using Computational Methods
en_US
ethz.grant
Combining Machine Learning and Molecular Dynamics to Predict Physicochemical Quantities of Molecules
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
Melville, NY
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02020 - Dep. Chemie und Angewandte Biowiss. / Dep. of Chemistry and Applied Biosc.::02515 - Laboratorium für Physikalische Chemie / Laboratory of Physical Chemistry::09458 - Riniker, Sereina Z. / Riniker, Sereina Z.
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02020 - Dep. Chemie und Angewandte Biowiss. / Dep. of Chemistry and Applied Biosc.::02515 - Laboratorium für Physikalische Chemie / Laboratory of Physical Chemistry::09458 - Riniker, Sereina Z. / Riniker, Sereina Z.
en_US
ethz.grant.agreementno
178762
ethz.grant.agreementno
ETH-34 17-2
ethz.grant.fundername
SNF
ethz.grant.fundername
ETHZ
ethz.grant.funderDoi
10.13039/501100001711
ethz.grant.funderDoi
10.13039/501100003006
ethz.grant.program
ETH Grants
ethz.grant.program
Projekte MINT
ethz.date.deposited
2020-12-21T10:00:08Z
ethz.source
FORM
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2020-12-22T13:36:04Z
ethz.rosetta.lastUpdated
2022-03-29T04:39:18Z
ethz.rosetta.versionExported
true
ethz.COinS
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