Faster access than browser!
31 relations: Acid dissociation constant, AMBER, Bennett acceptance ratio, Boltzmann constant, BOSS (molecular mechanics), CHARMM, Computational chemistry, Desmond (software), Drug discovery, Embarrassingly parallel, Force field (chemistry), GROMACS, MacroModel, Metropolis–Hastings algorithm, Molecular dynamics, Molecular mechanics, Mutagenesis, NAMD, Potential of mean force, Q (software), QM/MM, Quantum mechanics, Reaction coordinate, Solvent effects, Statistical mechanics, Temperature, Thermodynamic free energy, Thermodynamic integration, Tinker (software), Umbrella sampling, Virtual screening.
Acid dissociation constant
An acid dissociation constant, Ka, (also known as acidity constant, or acid-ionization constant) is a quantitative measure of the strength of an acid in solution.
New!!: Free energy perturbation and Acid dissociation constant · See more »
AMBER
Assisted Model Building with Energy Refinement (AMBER) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco.
New!!: Free energy perturbation and AMBER · See more »
Bennett acceptance ratio
The Bennett acceptance ratio method (sometimes abbreviated to BAR) is an algorithm for estimating the difference in free energy between two systems (usually the systems will be simulated on the computer).
New!!: Free energy perturbation and Bennett acceptance ratio · See more »
Boltzmann constant
The Boltzmann constant, which is named after Ludwig Boltzmann, is a physical constant relating the average kinetic energy of particles in a gas with the temperature of the gas.
New!!: Free energy perturbation and Boltzmann constant · See more »
BOSS (molecular mechanics)
Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3, and PDDG/PM3 quantum mechanics calculations.
New!!: Free energy perturbation and BOSS (molecular mechanics) · See more »
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.
New!!: Free energy perturbation and CHARMM · See more »
Computational chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems.
New!!: Free energy perturbation and Computational chemistry · See more »
Desmond (software)
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters.
New!!: Free energy perturbation and Desmond (software) · See more »
Drug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered.
New!!: Free energy perturbation and Drug discovery · See more »
Embarrassingly parallel
In parallel computing, an embarrassingly parallel workload or problem (also called perfectly parallel or pleasingly parallel) is one where little or no effort is needed to separate the problem into a number of parallel tasks.
New!!: Free energy perturbation and Embarrassingly parallel · See more »
Force field (chemistry)
In the context of molecular modeling, a force field (a special case of energy functions or interatomic potentials; not to be confused with force field in classical physics) refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics and molecular dynamics simulations.
New!!: Free energy perturbation and Force field (chemistry) · See more »
GROMACS
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.
New!!: Free energy perturbation and GROMACS · See more »
MacroModel
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers.
New!!: Free energy perturbation and MacroModel · See more »
Metropolis–Hastings algorithm
In statistics and in statistical physics, the Metropolis–Hastings algorithm is a Markov chain Monte Carlo (MCMC) method for obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult.
New!!: Free energy perturbation and Metropolis–Hastings algorithm · See more »
Molecular dynamics
Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules.
New!!: Free energy perturbation and Molecular dynamics · See more »
Molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems.
New!!: Free energy perturbation and Molecular mechanics · See more »
Mutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed, resulting in a mutation.
New!!: Free energy perturbation and Mutagenesis · See more »
NAMD
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model.
New!!: Free energy perturbation and NAMD · See more »
Potential of mean force
When examining a system computationally one may be interested to know 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).
New!!: Free energy perturbation and Potential of mean force · See more »
Q (software)
Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6).
New!!: Free energy perturbation and Q (software) · See more »
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of the QM (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins.
New!!: Free energy perturbation and QM/MM · See more »
Quantum mechanics
Quantum mechanics (QM; also known as quantum physics, quantum theory, the wave mechanical model, or matrix mechanics), including quantum field theory, is a fundamental theory in physics which describes nature at the smallest scales of energy levels of atoms and subatomic particles.
New!!: Free energy perturbation and Quantum mechanics · See more »
Reaction coordinate
In chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway.
New!!: Free energy perturbation and Reaction coordinate · See more »
Solvent effects
In chemistry, solvent effects are the influence of a solvent on chemical reactivity or molecular associations.
New!!: Free energy perturbation and Solvent effects · See more »
Statistical mechanics
Statistical mechanics is one of the pillars of modern physics.
New!!: Free energy perturbation and Statistical mechanics · See more »
Temperature
Temperature is a physical quantity expressing hot and cold.
New!!: Free energy perturbation and Temperature · See more »
Thermodynamic free energy
The thermodynamic free energy is the amount of work that a thermodynamic system can perform.
New!!: Free energy perturbation and Thermodynamic free energy · See more »
Thermodynamic integration
Thermodynamic integration is a method used to compare the difference in free energy between two given states (e.g., A and B) whose potential energies U_A and U_B have different dependences on the spatial coordinates.
New!!: Free energy perturbation and Thermodynamic integration · See more »
Tinker (software)
Tinker, stylized as TINKER, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers.
New!!: Free energy perturbation and Tinker (software) · See more »
Umbrella sampling
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.
New!!: Free energy perturbation and Umbrella sampling · See more »
Virtual screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
New!!: Free energy perturbation and Virtual screening · See more »
Redirects here:
Free-energy perturbation, Zwanzig equation.
References
[1] https://en.wikipedia.org/wiki/Free_energy_perturbation
