1.9k citations · 3.3k across the 21 of their papers we have counts for
23 papers
Force switching and potential shifting lead to significant cutoff dependence in alchemical free energies
Lindsey M. Whitmore, Yalda Ramezani, Sumit Sharma +1
The accurate treatment of long-range energy terms such as van der Waals interactions is crucial for reliable free energy calculations in molecular simulations. Methods like force s…
Replica exchange of expanded ensembles: A generalized ensemble approach with enhanced flexibility and parallelizability
Wei-Tse Hsu, Michael R. Shirts
Generalized ensemble methods such as Hamiltonian replica exchange (HREX) and expanded ensemble (EE) have been shown effective in free energy calculations for various contexts, give…
Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond
Kenichiro Takaba, Iván Pulido, Pavan Kumar Behara +11
The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is in…
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…