Literature DB >> 26317704

Variationally Optimized Free-Energy Flooding for Rate Calculation.

James McCarty1, Omar Valsson1,2, Pratyush Tiwary3, Michele Parrinello1,2.   

Abstract

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

Year:  2015        PMID: 26317704     DOI: 10.1103/PhysRevLett.115.070601

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


  6 in total

1.  Neural networks-based variationally enhanced sampling.

Authors:  Luigi Bonati; Yue-Yu Zhang; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-15       Impact factor: 11.205

2.  Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

Authors:  Michele Invernizzi; Omar Valsson; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-14       Impact factor: 11.205

3.  Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.

Authors:  Benjamin Pampel; Omar Valsson
Journal:  J Chem Theory Comput       Date:  2022-06-28       Impact factor: 6.578

4.  Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

Authors:  Patrick Shaffer; Omar Valsson; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2016-01-19       Impact factor: 11.205

5.  Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome.

Authors:  Jakub Rydzewski; Katarzyna Walczewska-Szewc; Sylwia Czach; Wieslaw Nowak; Krzysztof Kuczera
Journal:  J Phys Chem B       Date:  2022-03-31       Impact factor: 3.466

6.  Water regulates the residence time of Benzamidine in Trypsin.

Authors:  Narjes Ansari; Valerio Rizzi; Michele Parrinello
Journal:  Nat Commun       Date:  2022-09-16       Impact factor: 17.694

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.