Literature DB >> 26580515

Molecular Dynamics in the Multicanonical Ensemble: Equivalence of Wang-Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics.

Christoph Junghans1, Danny Perez1, Thomas Vogel1.   

Abstract

We show a direct formal relationship between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)], and statistical temperature molecular dynamics (STMD) [PRL 97, 050601 (2006)] that are the major work-horses for sampling from generalized ensembles. We demonstrate that STMD, itself derived from the Wang-Landau method, can be made indistinguishable from metadynamics. We also show that Gaussian kernels significantly improve the performance of STMD, highlighting the practical benefits of this improved formal understanding.

Entities:  

Year:  2014        PMID: 26580515     DOI: 10.1021/ct500077d

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


  4 in total

1.  Estimating thermodynamic expectations and free energies in expanded ensemble simulations: Systematic variance reduction through conditioning.

Authors:  Manuel Athènes; Pierre Terrier
Journal:  J Chem Phys       Date:  2017-05-21       Impact factor: 3.488

2.  Optimal updating magnitude in adaptive flat-distribution sampling.

Authors:  Cheng Zhang; Justin A Drake; Jianpeng Ma; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2017-11-07       Impact factor: 3.488

Review 3.  An Overview of Recent Standard and Accelerated Molecular Dynamics Simulations of Helium Behavior in Tungsten.

Authors:  Luis Sandoval; Danny Perez; Blas P Uberuaga; Arthur F Voter
Journal:  Materials (Basel)       Date:  2019-08-07       Impact factor: 3.623

4.  Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics.

Authors:  Niel M Henriksen; Andrew T Fenley; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2015-09-08       Impact factor: 6.006

  4 in total

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