Literature DB >> 11304387

Parallel excluded volume tempering for polymer melts.

A Bunker1, B Dünweg.   

Abstract

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts that makes use of both parallel tempering and large-scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large-scale Monte Carlo moves through attempted pivot and translation moves that reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as N=60 monomers, however at this chain length the large-scale Monte Carlo moves were ineffective. For even longer chains, the speedup becomes substantial, as observed from preliminary data for N=200. We also compare our scheme to the end bridging algorithm of Theodorou et al. For N=60, end bridging must allow a polydispersity of more than 10% in order to relax the end-to-end vector more quickly than our method. The comparison is, however, hampered by the fact that the end-to-end vector becomes a somewhat artificial quantity when one implements end bridging, and is perhaps no longer the slowest dynamic variable.

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Year:  2000        PMID: 11304387     DOI: 10.1103/PhysRevE.63.016701

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


  7 in total

1.  Proton strings and rings in atypical nucleation of ferroelectricity in ice.

Authors:  J Lasave; S Koval; A Laio; E Tosatti
Journal:  Proc Natl Acad Sci U S A       Date:  2020-12-21       Impact factor: 11.205

2.  Monte Carlo sampling for stochastic weight functions.

Authors:  Daan Frenkel; K Julian Schrenk; Stefano Martiniani
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-20       Impact factor: 11.205

3.  Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange.

Authors:  Tristan Bereau; Markus Deserno
Journal:  J Membr Biol       Date:  2014-10-14       Impact factor: 1.843

4.  Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics.

Authors:  Kiran Kumari; Burkhard Duenweg; Ranjith Padinhateeri; J Ravi Prakash
Journal:  Biophys J       Date:  2020-02-29       Impact factor: 4.033

5.  Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models.

Authors:  Steven Lettieri; Daniel M Zuckerman
Journal:  J Comput Chem       Date:  2011-11-25       Impact factor: 3.376

6.  More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.

Authors:  Tristan Bereau; Zun-Jing Wang; Markus Deserno
Journal:  J Chem Phys       Date:  2014-03-21       Impact factor: 3.488

Review 7.  Combined molecular algorithms for the generation, equilibration and topological analysis of entangled polymers: methodology and performance.

Authors:  Nikos Ch Karayiannis; Martin Kröger
Journal:  Int J Mol Sci       Date:  2009-11-23       Impact factor: 6.208

  7 in total

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