Literature DB >> 24476246

From metadynamics to dynamics.

Pratyush Tiwary1, Michele Parrinello1.   

Abstract

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple yet powerful method for calculating the rates of transition between different metastable states. The method does not rely on a previous knowledge of the transition states or reaction coordinates, as long as collective variables are known that can distinguish between the various stable minima in free energy space. We demonstrate that our method recovers the correct escape rates out of these stable states and also preserves the correct sequence of state-to-state transitions, with minimal extra computational effort needed over ordinary metadynamics. We apply the formalism to three different problems and in each case find excellent agreement with the results of long unbiased molecular dynamics runs.

Entities:  

Year:  2013        PMID: 24476246     DOI: 10.1103/PhysRevLett.111.230602

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  56 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

2.  Effect of material flexibility on the thermodynamics and kinetics of hydrophobically induced evaporation of water.

Authors:  Y Elia Altabet; Amir Haji-Akbari; Pablo G Debenedetti
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-13       Impact factor: 11.205

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.  Multiensemble Markov models of molecular thermodynamics and kinetics.

Authors:  Hao Wu; Fabian Paul; Christoph Wehmeyer; Frank Noé
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-25       Impact factor: 11.205

6.  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

7.  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

8.  Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling.

Authors:  Nuria Plattner; Stefan Doerr; Gianni De Fabritiis; Frank Noé
Journal:  Nat Chem       Date:  2017-06-05       Impact factor: 24.427

9.  Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane.

Authors:  Alexander J Pak; John M A Grime; Prabuddha Sengupta; Antony K Chen; Aleksander E P Durumeric; Anand Srivastava; Mark Yeager; John A G Briggs; Jennifer Lippincott-Schwartz; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2017-11-07       Impact factor: 11.205

10.  Catalytic Domains of Phosphodiesterase 5, 6, and 5/6 Chimera Display Differential Dynamics and Ligand Dissociation Energy Barriers.

Authors:  Jason G Pattis; Shaan Kamal; Boyang Li; Eric R May
Journal:  J Phys Chem B       Date:  2019-01-22       Impact factor: 2.991

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