Benchmark of Schemes for Multiscale Molecular Dynamics Simulations

N. Goga, M. N. Melo, A. J. Rzepiela, Alex de Vries, A. Hadar, S. J. Marrink*, Herman Berendsen

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)
225 Downloads (Pure)

Abstract

In multiscale molecular dynamics simulations the accuracy of detailed models is combined with the efficiency of a reduced representation. For several applications - namely those of sampling enhancement - it is desirable to combine fine-grained (FG) and coarse-grained (CG) approaches into a single hybrid approach with an adjustable mixing parameter. We present a benchmark of three algorithms that use a mixing of the two representation layers using a Lagrangian formalism. The three algorithms use three different approaches for keeping the particles at the FG level of representation together: 1) addition of forces, 2) mass scaling, and 3) temperature scaling. The benchmark is applied to liquid hexadecane and includes an evaluation of the average configurational entropy of the FG and CG subsystems. The temperature-scaling scheme achieved a 3-fold sampling speedup with little deviation of FG properties. The addition-of-forces scheme kept FG properties the best but provided little sampling speedup. The mass-scaling scheme yielded a 5-fold speedup but deviated the most from FG properties.

Original languageEnglish
Pages (from-to)1389-1398
Number of pages10
JournalJournal of Chemical Theory and Computation
Volume11
Issue number4
DOIs
Publication statusPublished - Apr-2015

Keywords

  • BIOMOLECULAR SIMULATIONS
  • ALGORITHMS
  • POTENTIALS
  • EFFICIENT
  • SYSTEMS
  • MODELS

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