148 citations · 745 across the 26 of their papers we have counts for
8 papers · 1 filter
Stepping up enhanced rate calculations with EATR-flooding
Nicodemo Mazzaferro, Willmor J Pena Ccoa, Pilar Cossio +1
Several recent methods have shown that it is possible to compute rate constants of very slow biomolecular processes using simulations where a time-dependent bias is added along one…
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio +1
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in confo…
Improved prediction of molecular response to pulling by combining force tempering with replica exchange methods
Yuvraj Singh, Glen M. Hocky
Small mechanical forces play important functional roles in many crucial cellular processes, including in the dynamical behavior of the cytoskeleton and in the regulation of osmotic…
Computing equilibrium free energies through a nonequilibrium quench
Kangxin Liu, Grant M. Rotskoff, Eric Vanden-Eijnden +1
Many methods to accelerate sampling of molecular configurations are based on the idea that temperature can be used to accelerate rare transitions. These methods typically compute e…
Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
In this work, we demonstrate that Linear Discriminant Analysis (LDA) applied to atomic positions in two different states of a biomolecule produces a good reaction coordinate betwee…
Size-and-Shape Space Gaussian Mixture Models for Structural Clustering of Molecular Dynamics Trajectories
Heidi Klem, Glen M. Hocky, Martin McCullagh
Determining the optimal number and identity of structural clusters from an ensemble of molecular configurations continues to be a challenge. Recent structural clustering methods ha…
A Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water
Paul B. Calio, Glen M. Hocky, Gregory A. Voth
Experiment Directed Simulations (EDS) is a method within a class of techniques seeking to improve molecular simulations by minimally biasing the system Hamiltonian to reproduce cer…
Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data
Andrew D. White, Chris Knight, Glen M. Hocky +1
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties…