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Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins

Posted June 8th, 2010 by pschmidtke
TitleClassical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins
Publication TypeJournal Article
Year of Publication2001
AuthorsGelpi, JL, Kalko SG, Barril X, Cirera J, de Cruz LX, Luque FJ, Orozco M
JournalProteins
Volume45
Issue4
Pagination428 - 437
Date Published2001/12/01/
KeywordsAcetylcholinesterase/chemistry/metabolism; Animals; Binding Sites; Catalase/chemistry/metabolism; Computer Simulation; Humans; Ions/chemistry/metabolism; Models, Chemical; Motion; Protein Conformation; Proteins/chemistry/metabolism; Static Electricity; Thymidine Kinase/chemistry/metabolism; Water/chemistry/metabolism
AbstractThe latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories.