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© Research
Publication : Journal of chemical theory and computation

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of chemical theory and computation - 20 Jun 2012

Deighan M, Bonomi M, Pfaendtner J

Link to Pubmed [PMID] – 26588950

J Chem Theory Comput 2012 Jul;8(7):2189-92

Herein, we report significant reduction in the cost of combined parallel tempering and metadynamics simulations (PTMetaD). The efficiency boost is achieved using the recently proposed well-tempered ensemble (WTE) algorithm. We studied the convergence of PTMetaD-WTE conformational sampling and free energy reconstruction of an explicitly solvated 20-residue tryptophan-cage protein (trp-cage). A set of PTMetaD-WTE simulations was compared to a corresponding standard PTMetaD simulation. The properties of PTMetaD-WTE and the convergence of the calculations were compared. The roles of the number of replicas, total simulation time, and adjustable WTE parameter γ were studied.

https://www.ncbi.nlm.nih.gov/pubmed/26588950