Literature DB >> 26580360

Assessing the Reliability of the Dynamics Reconstructed from Metadynamics.

Matteo Salvalaglio1,2, Pratyush Tiwary2,3, Michele Parrinello2,3.   

Abstract

Sampling a molecular process characterized by an activation free energy significantly larger than kBT is a well-known challenge in molecular dynamics simulations. In a recent work [Tiwary and Parrinello, Phys. Rev. Lett. 2013, 111, 230602], we have demonstrated that the transition times of activated molecular transformations can be computed from well-tempered metadynamics provided that no bias is deposited in the transition state region and that the set of collective variables chosen to enhance sampling does not display hysteresis. Ensuring though that these two criteria are met may not always be simple. Here we build on the fact that the times of escape from a long-lived metastable state obey Poisson statistics. This allows us to identify quantitative measures of trustworthiness of our calculation. We test our method on a few paradigmatic examples.

Year:  2014        PMID: 26580360     DOI: 10.1021/ct500040r

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  27 in total

1.  Role of water and steric constraints in the kinetics of cavity-ligand unbinding.

Authors:  Pratyush Tiwary; Jagannath Mondal; Joseph A Morrone; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-14       Impact factor: 11.205

Review 2.  Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling.

Authors:  M Bernetti; A Cavalli; L Mollica
Journal:  Medchemcomm       Date:  2017-01-30       Impact factor: 3.597

3.  Kramers turnover: From energy diffusion to spatial diffusion using metadynamics.

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-04-07       Impact factor: 3.488

4.  How wet should be the reaction coordinate for ligand unbinding?

Authors:  Pratyush Tiwary; B J Berne
Journal:  J Chem Phys       Date:  2016-08-07       Impact factor: 3.488

5.  Spectral gap optimization of order parameters for sampling complex molecular systems.

Authors:  Pratyush Tiwary; B J Berne
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-29       Impact factor: 11.205

6.  Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase.

Authors:  Xiakun Chu; Zucai Suo; Jin Wang
Journal:  Elife       Date:  2020-10-20       Impact factor: 8.140

Review 7.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

Review 8.  Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.

Authors:  Sergio Decherchi; Andrea Cavalli
Journal:  Chem Rev       Date:  2020-10-02       Impact factor: 60.622

Review 9.  Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).

Authors:  Sergei Yu Noskov; Tatiana K Rostovtseva; Adam C Chamberlin; Oscar Teijido; Wei Jiang; Sergey M Bezrukov
Journal:  Biochim Biophys Acta       Date:  2016-03-03

10.  Confronting pitfalls of AI-augmented molecular dynamics using statistical physics.

Authors:  Shashank Pant; Zachary Smith; Yihang Wang; Emad Tajkhorshid; Pratyush Tiwary
Journal:  J Chem Phys       Date:  2020-12-21       Impact factor: 3.488

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