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Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
Wei-Tse Hsu, Valerio Piomponi, Pascal T. Merz +2
Performing alchemical transformations, in which one molecular system is nonphysically changed to another system, is a popular approach adopted in performing free energy calculation…
How cooperatively folding are homopolymer molecular knots?
Christopher C. Walker, Theodore L. Fobe, Michael R. Shirts
Detailed thermodynamic analysis of complex systems with multiple stable configurational states allows for insight into the cooperativity of each individual transition. In this work…
Enhanced sampling methods for molecular dynamics simulations
Jérôme Hénin, Tony Lelièvre, Michael R. Shirts +2
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration…