Literature DB >> 18233794

Optimizing replica exchange moves for molecular dynamics.

Walter Nadler1, Ulrich H E Hansmann.   

Abstract

We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.

Year:  2007        PMID: 18233794     DOI: 10.1103/PhysRevE.76.057102

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


  7 in total

1.  Rapid equilibrium sampling initiated from nonequilibrium data.

Authors:  Xuhui Huang; Gregory R Bowman; Sergio Bacallado; Vijay S Pande
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-29       Impact factor: 11.205

2.  A generalized linear response framework for expanded ensemble and replica exchange simulations.

Authors:  Brian K Radak; Donghyuk Suh; Benoît Roux
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

3.  Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Authors:  Xiongwu Wu; Milan Hodoscek; Bernard R Brooks
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

4.  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

5.  From data to noise to data for mixing physics across temperatures with generative artificial intelligence.

Authors:  Yihang Wang; Lukas Herron; Pratyush Tiwary
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-04       Impact factor: 12.779

6.  The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state.

Authors:  Kaylyn M Oshaben; Reza Salari; Darrell R McCaslin; Lillian T Chong; W Seth Horne
Journal:  Biochemistry       Date:  2012-11-13       Impact factor: 3.162

7.  Equilibrium molecular thermodynamics from Kirkwood sampling.

Authors:  Sandeep Somani; Yuko Okamoto; Andrew J Ballard; David J Wales
Journal:  J Phys Chem B       Date:  2015-05-12       Impact factor: 2.991

  7 in total

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