Related Experiment Video
Updated: Feb 22, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches
Published on: October 13, 2022
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange
Agnieszka S Karczyńska1,2,3, Cezary Czaplewski1, Paweł Krupa1,4
1Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk, 80-308, Poland.
Abstract:
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.
More Related Videos
Related Concept Videos
Molecular Chaperones and Protein Folding
The...
Cooperative Allosteric Transitions
Cooperative Allosteric Transitions
Cooperative Allosteric Transitions
Protein Folding Quality Check in the RER
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

