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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.
In thermodynamic integration, the free energy difference is calculated by defining a thermodynamic path between the states and integrating over ensemble-averaged enthalpy changes along the path. Such paths can either be real chemical processes or alchemical processes. An example alchemical process is the Kirkwood's coupling parameter method. [1]
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen , and is now maintained by contributors in universities and research centers worldwide.
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.
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.
High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods Free open source, Educational Community License version 2.0 NWChem: Protein Local Optimization Program: No Yes Yes Yes Yes No No No No Helix, loop, and side chain optimizing, fast energy minimizing Proprietary: PLOP wiki ...
Parallel tempering, in physics and statistics, is a computer simulation method typically used to find the lowest energy state of a system of many interacting particles.It addresses the problem that at high temperatures, one may have a stable state different from low temperature, whereas simulations at low temperatures may become "stuck" in a metastable state.