INVESTIGADORES
MILLÁN RaÚl Daniel
congresos y reuniones científicas
Título:
Enhanced Sampling of Molecular Dynamics Simulations with Self-learning Collective Variables
Autor/es:
BEHROOZ HASHEMIAN; DANIEL MILLÁN; MARINO ARROYO
Lugar:
Belfast
Reunión:
Workshop; Enhancing molecular simulations with PLUMED; 2014
Institución organizadora:
CECAM - Centre Européen de Calcul Atomique et Moléculaire
Resumen:
One of the main outstanding issues in molecular dynamics simulations is accessing the relevant time-scales for conformational transitions in functional molecules, as a result of metastability. This makes it difficult to connect simulations with experimental observables. To overcome this issue, a number of enhanced sampling methods have been proposed, such as metadynamics and adaptive biasing force. However the effectiveness of these methods strongly relies on the choice of a good set of collective variables (CVs), which need to compactly describe molecular conformations, capture metastability, and be differentiable. To this end, Spiwok et al employ path collective variable (PCV) to define smooth CVs from the output of Isomap and report on promising but not converged metadynamics simulations and Tribello et al introduce a field-overlap procedure to combine sketch-map with metadynamics. Here, we present a self-learning methodology based on manifold learning techniques that, starting from pre-existing computational or experimental ensembles representative of the conformational variability, builds smooth and nonlinear data-driven collective variables (SandCV) and integrate them with enhanced sampling methods. SandCV is founded on an intrinsic manifold model for the molecular system. This methodology can deal seamlessly with intrinsic manifolds of complex topology described with multiple parameterization charts. SandCV is independent of the enhanced sampling method, minimally invasive with respect to the underlying molecular dynamics code and is going to be implemented in PLUMED to be available for the scientific community.