Literature DB >> 26183423

Self-guided Langevin dynamics via generalized Langevin equation.

Xiongwu Wu1, Bernard R Brooks1, Eric Vanden-Eijnden2.   

Abstract

Self-guided Langevin dynamics (SGLD) is a molecular simulation method that enhances conformational search and sampling via acceleration of the low frequency motions of the system. This acceleration is produced via introduction of a guiding force which breaks down the detailed-balance property of the dynamics, implying that some reweighting is necessary to perform equilibrium sampling. Here, we eliminate the need of reweighing and show that the NVT and NPT ensembles are sampled exactly by a new version of self-guided motion involving a generalized Langevin equation (GLE) in which the random force is modified so as to restore detailed-balance. Through the examples of alanine dipeptide and argon liquid, we show that this SGLD-GLE method has enhanced conformational sampling capabilities compared with regular Langevin dynamics (LD) while being of comparable computational complexity. In particular, SGLD-GLE is fully size extensive and can be used in arbitrarily large systems, making it an appealing alternative to LD.
© 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Entities:  

Keywords:  canonical ensemble; conformational sampling; generalized Langevin equation; molecular simulation; self-guided Langevin dynamics

Mesh:

Substances:

Year:  2015        PMID: 26183423      PMCID: PMC4715807          DOI: 10.1002/jcc.24015

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  10 in total

1.  Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2011-11-28       Impact factor: 3.488

2.  Characterizing the denatured state of human prion 121-230.

Authors:  Cheng-I Lee; Nai-yuan Chang
Journal:  Biophys Chem       Date:  2010-05-15       Impact factor: 2.352

3.  Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation.

Authors:  Pushkar Y Pendse; Bernard R Brooks; Jeffery B Klauda
Journal:  J Mol Biol       Date:  2010-09-25       Impact factor: 5.469

Review 4.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

5.  Langevin equation with colored noise for constant-temperature molecular dynamics simulations.

Authors:  Michele Ceriotti; Giovanni Bussi; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2009-01-14       Impact factor: 9.161

6.  Open science grid study of the coupling between conformation and water content in the interior of a protein.

Authors:  Ana Damjanović; Benjamin T Miller; Torre J Wenaus; Petar Maksimović; Bertrand García-Moreno E; Bernard R Brooks
Journal:  J Chem Inf Model       Date:  2008-10-04       Impact factor: 4.956

7.  Toward canonical ensemble distribution from self-guided Langevin dynamics simulation.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2011-04-07       Impact factor: 3.488

8.  Self-guided Langevin dynamics study of regulatory interactions in NtrC.

Authors:  Ana Damjanović; Bertrand García-Moreno E; Bernard R Brooks
Journal:  Proteins       Date:  2009-09

9.  Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.

Authors:  Xiongwu Wu; Ana Damjanovic; Bernard R Brooks
Journal:  Adv Chem Phys       Date:  2012-01-31       Impact factor: 1.000

10.  Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study.

Authors:  Ana Damjanović; Xiongwu Wu; Bertrand García-Moreno E; Bernard R Brooks
Journal:  Biophys J       Date:  2008-07-18       Impact factor: 4.033

  10 in total
  20 in total

1.  Reformulation of the self-guided molecular simulation method.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Chem Phys       Date:  2020-09-07       Impact factor: 3.488

2.  Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

Authors:  Xiongwu Wu; Juyong Lee; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2016-10-18       Impact factor: 2.991

3.  Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.

Authors:  Naohiro Nishikawa; Kyungreem Han; Xiongwu Wu; Florentina Tofoleanu; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

4.  Molecular dynamics simulations of lipid nanodiscs.

Authors:  Mohsen Pourmousa; Richard W Pastor
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-05-03       Impact factor: 3.747

5.  Atomic Resolution Cryo-EM Structure of β-Galactosidase.

Authors:  Alberto Bartesaghi; Cecilia Aguerrebere; Veronica Falconieri; Soojay Banerjee; Lesley A Earl; Xing Zhu; Nikolaus Grigorieff; Jacqueline L S Milne; Guillermo Sapiro; Xiongwu Wu; Sriram Subramaniam
Journal:  Structure       Date:  2018-05-10       Impact factor: 5.006

6.  Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

Authors:  Yinglong Miao; J Andrew McCammon
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

7.  Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.

Authors:  Laurentiu Spiridon; David D L Minh
Journal:  J Chem Theory Comput       Date:  2017-09-27       Impact factor: 6.006

8.  Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins.

Authors:  Xiongwu Wu; Bernard R Brooks
Journal:  J Phys Chem B       Date:  2018-06-01       Impact factor: 2.991

Review 9.  Ensemble Docking in Drug Discovery.

Authors:  Rommie E Amaro; Jerome Baudry; John Chodera; Özlem Demir; J Andrew McCammon; Yinglong Miao; Jeremy C Smith
Journal:  Biophys J       Date:  2018-03-30       Impact factor: 4.033

Review 10.  Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.

Authors:  Zhiye Tang; Christopher C Roberts; Chia-En A Chang
Journal:  Front Biosci (Landmark Ed)       Date:  2017-01-01
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