Calculating free energies using average force

By Eric F Darve, Andrew Pohorille. 2001

967 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Statistical and Nonlinear Physics

View Paper: https://www.semanticscholar.org/paper/3d3b16bde3817ae07b76730fa37e139708dbbdc8

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In Atomic and Molecular Physics, and Optics

In Molecular Biology

In Statistical and Nonlinear Physics

Citations in the corpus

Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, methodology): “Free-energy barriers can be overcome by depositing harmonic potentials, as is done in US (b); by applying a time-dependent bias that yields a Hamiltonian bereft of an average force along ξ ( x ), as is done in ABF, or its extended-Lagrangian variant, eABF (c); or by flooding valleys by means of Gaus”
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask (2014, methodology): “To increase the e ﬃ ciency of exploring the transition coordinate in adaptive biasing force 19 or umbrella sampling, 11 it is common to break down the transition path into a series of sequential strata or windows .”
Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems (2014, positive): “Darve and Phorrille [45] described the method as “filling the free energywells with computational sand” (see Fig.”
Scalable molecular dynamics with NAMD (2005, methodology): “This includes, among others, the intramolecular folding of a short peptide, the partitioning of small solutes across an aqueous interface and the intermolecular association of neutral and ionic species [92,93].”
Merrimac: Supercomputing with Streams (2003, methodology): “StreamMD is a molecular dynamics solver [15, 16] that is based on solving Newton’s equations of motion.”
Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0] (2022, methodology): “1 Standard ABF In the original formulation of ABF [216, 219, 220], the collective force is calculated based on a constraint force calculation.”
Protein storytelling through physics (2020, background): “Advances are coming from enhanced sampling methods, such as metadynamics ( 34 ), replica exchange molecular dynamics (REMD) ( 35 ), simulated annealing ( 36 ), adaptive force biasing ( 37 ), and umbrella sampling ( 38 ) [for reviews,see( 39 , 40 ),andforthebasicconcepts see ( 21 , 41 )].”
Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. (2016, methodology): “The most popular methods are the gradient-based Umbrella Integration [67, 68], the Blue Moon method [69, 70], the Adaptive Biasing Force (ABF) method [71, 72], and the histogram-based Metadynamics [73–75].”