title: Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.
abstract: Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.
authors.affiliation: Department of Biochemistry and Microbiology, Institute of Chemical Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic. spiwokv@vscht.cz
authors.forename: Vojtěch
authors.initials: V
authors.lastname: Spiwok
authors.forename: Blanka
authors.initials: B
authors.lastname: Králová
mesh_terms: D000465:Algorithms; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009038:Motion; D017711:Nonlinear Dynamics; D013816:Thermodynamics