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Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins
Author(s) -
Karczyńska Agnieszka S.,
Czaplewski Cezary,
Krupa Paweł,
Mozolewska Magdalena A.,
Joo Keehyoung,
Lee Jooyoung,
Liwo Adam
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25070
Subject(s) - ergodicity , replica , molecular dynamics , statistical physics , hamiltonian (control theory) , template , gaussian , canonical ensemble , brownian dynamics , physics , computer science , biological system , mathematics , chemistry , computational chemistry , brownian motion , quantum mechanics , monte carlo method , mathematical optimization , biology , art , statistics , visual arts , programming language
Molecular simulations restrained to single or multiple templates are commonly used in protein‐structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template‐restrained canonical molecular dynamics (MD), multiplexed replica‐exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse‐grained UNRES force field on nine selected proteins, with pseudo‐harmonic log‐Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non‐ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor‐quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc.