Normal mode partitioning of Langevin dynamics for biomolecules.

The Journal of Chemical Physics
Christopher R SweetJesús A Izaguirre

Abstract

We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square of the mode frequency. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems, NML gives a twofold improvement in efficiency over plain Langevin dynamics for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for ...Continue Reading

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Citations

Jan 14, 2011·Quarterly Reviews of Biophysics·Tamar SchlickXia Xiao
Jun 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Eric DarveAmirali Kia
Aug 3, 2011·The Journal of Chemical Physics·D I Zhukhovitskii
Apr 3, 2012·The Journal of Chemical Physics·Emanuel PeterStephan A Baeurle
Jan 12, 2011·The Journal of Chemical Physics·Joseph A MorroneB J Berne
Feb 2, 2011·The Journal of Chemical Physics·A SingharoyP Ortoleva
Nov 18, 2010·Current Opinion in Structural Biology·Gregory R BowmanVijay S Pande
Jul 23, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Samuel Coulbourn FloresRuss Biagio Altman
Feb 27, 2016·Journal of Chemical Theory and Computation·Yunjie ChenBenoit Roux
Aug 2, 2011·Progress in Biophysics and Molecular Biology·Harshad JoshiPeter J Ortoleva
Nov 3, 2009·Journal of Computational Chemistry·Trevor CickovskiJesús A Izaguirre
Dec 3, 2016·The Journal of Chemical Physics·Lina MaChun Liu
Jun 8, 2010·Journal of Chemical Theory and Computation·Joseph A MorroneB J Berne
Feb 24, 2012·The Journal of Physical Chemistry. B·Abhishek SingharoyPeter J Ortoleva
Jun 5, 2012·Journal of Chemical Theory and Computation·Abhishek SingharoyPeter J Ortoleva
Jan 15, 2013·Journal of Chemical Theory and Computation·Christopher L McClendonMatthew P Jacobson
Jan 18, 2014·Journal of Chemical Theory and Computation·James C SweetJesús A Izaguirre

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Methods Mentioned

BETA
PCA

Software Mentioned

CHARMM
NAB
NML
NMA
SHAKE
PROTOMOL
LLMOD
RESPA
ElNémo
SMD

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