30 citations · 53 across the 4 of their papers we have counts for
5 papers
A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4
Bradley M. Dickson, Parker W de Waal, Zachary H Ramjan +2
In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We…
-tempered metadynamics: Artifact independent convergence times for wide hills
Bradley M. Dickson
Recent analysis of well-tempered metadynamics (WTmetaD) showed that it converges without mollification artifacts in the bias potential. Here we explore how metadynamics heals molli…
The entropic lock and key of the histone code
Bradley M. Dickson, Dmitri B. Kireev
The intricate pattern of chemical modifications on DNA and histones, the "histone code", is considered to be a key gene regulation factor. Multivalency is seen by many as an essent…
Approaching a parameter-free metadynamics
Bradley M. Dickson
We present a unique derivation of metadynamics. The starting point for the derivation is an on-the-fly reweighting scheme but through an approximation we recover the standard metad…
Free energy calculations: An efficient adaptive biasing potential method
Bradley M. Dickson, Frederic Legoll, Tony Lelievre +2
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an appro…