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Umbrella sampling is a technique in computational physics and chemistry, used to improve sampling of a system (or different systems) where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Torrie and Valleau in 1977. [1]
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology.It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape.
When examining a system computationally one may be interested in knowing how the free energy changes as a function of some inter- or intramolecular coordinate (such as the distance between two atoms or a torsional angle). The free energy surface along the chosen coordinate is referred to as the potential of mean force (PMF). If the system of ...
Umbrella sampling is another free-energy calculation technique that is typically used for calculating the free-energy change associated with a change in "position" coordinates as opposed to "chemical" coordinates, although umbrella sampling can also be used for a chemical transformation when the "chemical" coordinate is treated as a dynamic ...
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used together with analysis and visualization tools VMD, HTMD, and ...
Importance sampling is a variance reduction technique that can be used in the Monte Carlo method. The idea behind importance sampling is that certain values of the input random variables in a simulation have more impact on the parameter being estimated than others.
The free energy surface can therefore be approximated directly from the bias potential (as done in the metadynamics method) or the bias potential can be used for umbrella sampling (as done in metadynamics with umbrella sampling corrections [10] and local elevation umbrella sampling [7] methods) to obtain more accurate free energies.
Rare event sampling is an umbrella term for a group of computer simulation methods intended to selectively sample 'special' regions of the dynamic space of systems which are unlikely to visit those special regions through brute-force simulation.