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© Research
Publication : Journal of chemical theory and computation

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of chemical theory and computation - 06 Sep 2018

Prakash A, Fu CD, Bonomi M, Pfaendtner J

Link to Pubmed [PMID] – 30075630

J Chem Theory Comput 2018 Oct;14(10):4985-4990

Molecular simulations of systems with multiple copies of identical atoms or molecules may require the biasing of numerous, degenerate collective variables (CVs) to accelerate sampling. Recently, a variation of metadynamics (MetaD) named parallel bias metadynamics (PBMetaD) has been shown to make biasing of many CVs more tractable. We extended the PBMetaD scheme so that it partitions degenerate CVs into families that share the same bias potential, consequently expediting convergence of the free-energy landscape. We tested our method, named parallel bias metadynamics with partitioned families, on 3, 21, and 78 CV systems and obtained an approximately proportional increase in convergence speed compared to standard PBMetaD.

https://www.ncbi.nlm.nih.gov/pubmed/30075630