Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping-Reference-Cited by-同舟云学术

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Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping

Published:2013-08-22 Issue:9 Volume:9 Page:4215-4224
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Plattner Nuria¹,Doll J. D.²,Meuwly Markus³

Affiliation:

1. Department of Mathematics and Computer Science, Free University Berlin, Arnimallee 6, 14195 Berlin, Germany

2. Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States

3. Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/ct400355g

Reference37 articles.

1. Molecular dynamics simulations of biomolecules

2. Long-timescale simulation methods

3. Molecular dynamics and protein function

4. Parallel tempering: Theory, applications, and new perspectives

5. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

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1. Path sampling with memory reduction and replica exchange to reach long permeation timescales;Biophysical Journal;2023-07

2. Efficient Interrogation of the Kinetic Barriers Demarcating Catalytic States of a Tyrosine Kinase with Optimal Physical Descriptors and Mixture Models;ChemPhysChem;2022-12-09

3. Exchanging Replicas with Unequal Cost, Infinitely and Permanently;The Journal of Physical Chemistry A;2022-11-17

4. Infinite Swapping Algorithm for Training Restricted Boltzmann Machines;Springer Proceedings in Mathematics & Statistics;2020

5. Replica sub‐permutation method for molecular dynamics and monte carlo simulations;Journal of Computational Chemistry;2019-07-31

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