Literature DB >> 17358396

Generalized ensemble and tempering simulations: a unified view.

Walter Nadler1, Ulrich H E Hansmann.   

Abstract

From the underlying master equations we derive one-dimensional stochastic processes that describe generalized ensemble simulations as well as tempering (simulated and parallel) simulations. The representations obtained are either in the form of a one-dimensional Fokker-Planck equation or a hopping process on a one-dimensional chain. In particular, we discuss the conditions under which these representations are valid approximate Markovian descriptions of the random walk in order parameter or control parameter space. They allow a unified discussion of the stationary distribution on, as well as of the stationary flow across, each space. We demonstrate that optimizing the flow is equivalent to minimizing the first passage time for crossing the space and discuss the consequences of our results for optimizing simulations. Finally, we point out the limitations of these representations under conditions of broken ergodicity.

Year:  2007        PMID: 17358396     DOI: 10.1103/PhysRevE.75.026109

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  16 in total

1.  Comparison of sampling efficiency between simulated tempering and replica exchange.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2008-10-07       Impact factor: 3.488

2.  Error and efficiency of simulated tempering simulations.

Authors:  Edina Rosta; Gerhard Hummer
Journal:  J Chem Phys       Date:  2010-01-21       Impact factor: 3.488

3.  Error and efficiency of replica exchange molecular dynamics simulations.

Authors:  Edina Rosta; Gerhard Hummer
Journal:  J Chem Phys       Date:  2009-10-28       Impact factor: 3.488

4.  Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Authors:  Jason A Wallace; Jana K Shen
Journal:  J Chem Phys       Date:  2012-11-14       Impact factor: 3.488

5.  Folding simulations of the A and B domains of protein G.

Authors:  Maksim Kouza; Ulrich H E Hansmann
Journal:  J Phys Chem B       Date:  2012-01-24       Impact factor: 2.991

6.  Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.

Authors:  Koushik Kasavajhala; Kenneth Lam; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2020-11-03       Impact factor: 6.006

7.  Multifunnel Landscape of the Fold-Switching Protein RfaH-CTD.

Authors:  Nathan A Bernhardt; Ulrich H E Hansmann
Journal:  J Phys Chem B       Date:  2018-01-24       Impact factor: 2.991

8.  Transmembrane helix assembly by window exchange umbrella sampling.

Authors:  Soohyung Park; Taehoon Kim; Wonpil Im
Journal:  Phys Rev Lett       Date:  2012-03-08       Impact factor: 9.161

9.  Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.

Authors:  Soohyung Park; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2012-11-19       Impact factor: 6.006

10.  Modeling Structural Flexibility of Proteins with Go-Models.

Authors:  Ping Jiang; Ulrich H E Hansmann
Journal:  J Chem Theory Comput       Date:  2012-06-12       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.