From A to B in free energy space.

By D. Branduardi, Francesco Luigi Gervasio, Michele Parrinello. Journal of Chemical Physics, 2007

568 citations recorded by the source corpus.

The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/9b379603a3d8fa01ebd43fca7655fe345156eee9

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Citations in the corpus

Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, background): “101 Independently, path-collective variables 102 are available in Tcl as scripted functions.”
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013, methodology): “If the snapshots are disposed along a putative path connecting two experimental structures, this CV can be used as a path CV to monitor and bias the progression along the path [182].”