Literature DB >> 16144000

Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.

Giovanni Ciccotti1, Raymond Kapral, Eric Vanden-Eijnden.   

Abstract

We give a new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling. This generalizes to the vectorial case a formula first derived by Ruiz-Montero et al. for a scalar reaction coordinate. We also discuss how to compute this conditional average by means of constrained stochastic dynamics which, unlike the usual constrained molecular dynamics, introduces no bias. Finally, we give a new perspective on bias removal by using constrained molecular dynamics.

Year:  2005        PMID: 16144000     DOI: 10.1002/cphc.200400669

Source DB:  PubMed          Journal:  Chemphyschem        ISSN: 1439-4235            Impact factor:   3.102


  20 in total

1.  Solvent effect on cation-π interactions with Al3+.

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Journal:  J Mol Model       Date:  2012-05-13       Impact factor: 1.810

2.  Exact Relation between Potential of Mean Force and Free-Energy Profile.

Authors:  Kin-Yiu Wong; Darrin M York
Journal:  J Chem Theory Comput       Date:  2012-09-06       Impact factor: 6.006

Review 3.  Path Sampling Methods for Enzymatic Quantum Particle Transfer Reactions.

Authors:  M W Dzierlenga; M J Varga; S D Schwartz
Journal:  Methods Enzymol       Date:  2016-06-16       Impact factor: 1.600

4.  A benchmark for reaction coordinates in the transition path ensemble.

Authors:  Wenjin Li; Ao Ma
Journal:  J Chem Phys       Date:  2016-04-07       Impact factor: 3.488

5.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

6.  Value of Temporal Information When Analyzing Reaction Coordinates.

Authors:  Piao Ma; Ron Elber; Dmitrii E Makarov
Journal:  J Chem Theory Comput       Date:  2020-09-08       Impact factor: 6.006

7.  Gaussian-mixture umbrella sampling.

Authors:  Paul Maragakis; Arjan van der Vaart; Martin Karplus
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

8.  Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

Authors:  Yinglong Miao; J Andrew McCammon
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

9.  Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.

Authors:  Wenwei Zheng; Mary A Rohrdanz; Cecilia Clementi
Journal:  J Phys Chem B       Date:  2013-08-07       Impact factor: 2.991

10.  Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces.

Authors:  Jeffrey A Herron; Yoshitada Morikawa; Manos Mavrikakis
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-08       Impact factor: 11.205

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