Multiscale macromolecular simulation: Role of evolving ensembles

Abhishek Singharoy, H. Joshi, P. J. Ortoleva

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.

Original languageEnglish (US)
Pages (from-to)2638-2649
Number of pages12
JournalJournal of Chemical Information and Modeling
Volume52
Issue number10
DOIs
StatePublished - Oct 22 2012
Externally publishedYes

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simulation
Atoms
Structural dynamics
Program processors
History
efficiency
history
Hot Temperature
time

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

Cite this

Multiscale macromolecular simulation : Role of evolving ensembles. / Singharoy, Abhishek; Joshi, H.; Ortoleva, P. J.

In: Journal of Chemical Information and Modeling, Vol. 52, No. 10, 22.10.2012, p. 2638-2649.

Research output: Contribution to journalArticle

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