Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00873
Abstract: Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. A class of such enhanced sampling methods… read more here.
Keywords: learning collective; enhanced sampling; reweighted manifold; manifold learning ... See more keywords
Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.899805
Abstract: The dissociation rate (k off) associated with ligand unbinding events from proteins is a parameter of fundamental importance in drug design. Here we review recent major advancements in molecular simulation methodologies for the prediction of… read more here.
Keywords: sampling simulations; enhanced sampling; binding kinetics; ligand binding ... See more keywords
Umbrella Sampling Simulations of Carbon Nanoparticles Crossing Immiscible Solvents
Sign Up to like & getrecommendations! Published in 2022 at "Molecules"
DOI: 10.3390/molecules27030956
Abstract: We use molecular dynamics to compute the free energy of carbon nanoparticles crossing a hydrophobic–hydrophilic interface. The simulations are performed on a biphasic system consisting of immiscible solvents (i.e., cyclohexane and water). We solvate a… read more here.
Keywords: carbon; umbrella sampling; immiscible solvents; carbon nanoparticles ... See more keywords