Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Periole, X and Mark, AE (2007) Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. Journal of Chemical Physics, 126 1: 014903-1-014903-11. doi:10.1063/1.2404954

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Author Periole, X
Mark, AE
Title Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
Journal name Journal of Chemical Physics   Check publisher's open access policy
ISSN 0021-9606
Publication date 2007-01-04
Sub-type Article (original research)
DOI 10.1063/1.2404954
Open Access Status File (Publisher version)
Volume 126
Issue 1
Start page 014903-1
End page 014903-11
Total pages 11
Place of publication Melville
Publisher Amer Inst Physics
Collection year 2008
Language eng
Subject C1
780103 Chemical sciences
Abstract Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comparison of conventional MD and temperature replica exchange MD (T-REMD) simulations of a beta-heptapeptide in explicit solvent. This system has previously been shown to undergo reversible folding on the time scales accessible to MD simulation and thus allows a direct one-to-one comparison of efficiency. The primary properties compared are the free energy of folding and the relative populations of different conformers as a function of temperature. It is found that to achieve a similar degree of precision T-REMD simulations starting from a random set of initial configurations were approximately an order of magnitude more computationally efficient than a single 800 ns conventional MD simulation for this system at the lowest temperature investigated (275 K). However, whereas it was found that T-REMD simulations are more than four times more efficient than multiple independent MD simulations at one temperature (300 K) the actual increase in conformation sampling was only twofold. The overall gain in efficiency using REMD resulted primarily from the ordering of different conformational states over temperature, as opposed to a large increase of conformational sampling. It is also shown that in this system exchanges are accepted primarily based on (random) fluctuations within the solvent and are not strongly correlated with the instantaneous peptide conformation raising questions in regard to the efficiency of T-REMD in larger systems.
Keyword Physics, Atomic, Molecular & Chemical
Molecular-dynamics Simulations
Free-energy Landscape
Generalized-ensemble Algorithms
Structure Prediction
Beta-hairpin
Water
Kinetics
Model
Chain
Thermodynamics
Q-Index Code C1
Q-Index Status Confirmed Code

 
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Created: Tue, 19 Feb 2008, 02:01:41 EST