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MTD closely resembles a number of newer methods such as adaptively biased molecular dynamics, [2] adaptive reaction coordinate forces [3] and local elevation umbrella sampling. [4] More recently, both the original and well-tempered metadynamics [ 5 ] were derived in the context of importance sampling and shown to be a special case of the ...
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]
Umbrella sampling is a related free energy method. It adds a bias to the potential energy. It adds a bias to the potential energy. In the limit of an infinite strong bias it is equivalent to thermodynamic integration.
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 ...
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 ...
Gosai et al. have also used umbrella sampling simulations to show that potential of mean force decreases between thrombin and its aptamer (a protein-ligand complex) under the effect of electrical fields.
Umbrella sampling is used to move the system along the desired reaction coordinate by varying, for example, the forces, distances, and angles manipulated in the simulation. Through umbrella sampling, all of the system's configurations—both high-energy and low-energy—are adequately sampled.
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.