Literature DB >> 19518393

From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering.

Ayori Mitsutake1, Yuko Okamoto.   

Abstract

We discuss multidimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential-energy function E0 by adding any physical quantity V of interest as a new energy term with a coupling constant lambda. We then perform a multidimensional multicanonical simulation where a random walk in E0 and V spaces is realized. We can alternately perform a multidimensional simulated-tempering simulation where a random walk in temperature T and parameter lambda is realized. The results of the multidimensional replica-exchange simulations can be used to determine the weight factors for these multidimensional multicanonical and simulated-tempering simulations.

Year:  2009        PMID: 19518393     DOI: 10.1103/PhysRevE.79.047701

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


  5 in total

1.  Generalized simulated tempering for exploring strong phase transitions.

Authors:  Jaegil Kim; John E Straub
Journal:  J Chem Phys       Date:  2010-10-21       Impact factor: 3.488

2.  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

3.  Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

Authors:  Wei Jiang; Milan Hodoscek; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2009-10-01       Impact factor: 6.006

Review 4.  Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).

Authors:  Sergei Yu Noskov; Tatiana K Rostovtseva; Adam C Chamberlin; Oscar Teijido; Wei Jiang; Sergey M Bezrukov
Journal:  Biochim Biophys Acta       Date:  2016-03-03

5.  Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

Authors:  Wei Jiang; James C Phillips; Lei Huang; Mikolai Fajer; Yilin Meng; James C Gumbart; Yun Luo; Klaus Schulten; Benoît Roux
Journal:  Comput Phys Commun       Date:  2014-03       Impact factor: 4.390

  5 in total

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