Literature DB >> 26574405

Well-Tempered Variational Approach to Enhanced Sampling.

Omar Valsson1,2, Michele Parrinello1,2.   

Abstract

We propose a simple yet effective iterative scheme that allows us to employ the well-tempered distribution as a target distribution for the collective variables in our recently introduced variational approach to enhanced sampling and free energy calculations [ Valsson and Parrinello Phys. Rev. Lett. 2014 , 113 , 090601 ]. The performance of the scheme is evaluated for the three-dimensional free energy surface of alanine tetrapeptide where the convergence can be rather poor when employing the uniform target distribution. Using the well-tempered target distribution on the other hand results in a significant improvement in convergence. The results observed in this paper indicate that the well-tempered distribution is in most cases the preferred and recommended choice for the target distribution in the variational approach.

Year:  2015        PMID: 26574405     DOI: 10.1021/acs.jctc.5b00076

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


  7 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.  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

4.  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

5.  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

6.  Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.

Authors:  Hongrui Wang; Hongwei Liu; Leixin Cai; Caixia Wang; Qiang Lv
Journal:  BMC Bioinformatics       Date:  2017-07-10       Impact factor: 3.169

7.  Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics.

Authors:  Yong Wang; João Miguel Martins; Kresten Lindorff-Larsen
Journal:  Chem Sci       Date:  2017-07-12       Impact factor: 9.825

  7 in total

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