Literature DB >> 16486650

Resolution exchange simulation.

Edward Lyman1, F Marty Ytreberg, Daniel M Zuckerman.   

Abstract

We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution--i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.

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Year:  2006        PMID: 16486650     DOI: 10.1103/PhysRevLett.96.028105

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


  49 in total

1.  Generalized replica exchange method.

Authors:  Jaegil Kim; Thomas Keyes; John E Straub
Journal:  J Chem Phys       Date:  2010-06-14       Impact factor: 3.488

2.  Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin.

Authors:  Wenfei Li; Shoji Takada
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

3.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

4.  Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.

Authors:  Adrian E Roitberg; Asim Okur; Carlos Simmerling
Journal:  J Phys Chem B       Date:  2007-02-15       Impact factor: 2.991

5.  Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

Authors:  Bin W Zhang; David Jasnow; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2007-11-01       Impact factor: 11.205

6.  A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation.

Authors:  Daniel M Zuckerman; Edward Lyman
Journal:  J Chem Theory Comput       Date:  2006       Impact factor: 6.006

7.  Optimal replica exchange method combined with Tsallis weight sampling.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2009-04-14       Impact factor: 3.488

8.  A black-box re-weighting analysis can correct flawed simulation data.

Authors:  F Marty Ytreberg; Daniel M Zuckerman
Journal:  Proc Natl Acad Sci U S A       Date:  2008-06-10       Impact factor: 11.205

9.  Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.

Authors:  Ian J Nessler; Jacob M Litman; Michael J Schnieders
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

10.  Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Authors:  Asim Okur; Benjamin T Miller; Keehyoung Joo; Jooyoung Lee; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2013-02-01       Impact factor: 6.006

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