Abalone (molecular mechanics)
Encyclopedia
Molecular dynamics
Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
and molecular graphics
Molecular graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
program for simulations of bio-molecules in a periodic boundary conditions
Periodic boundary conditions
In mathematical models and computer simulations, periodic boundary conditions are a set of boundary conditions that are often used to simulate a large system by modelling a small part that is far from its edge...
in explicit water (Flexible SPC
Flexible SPC water model
The Flexible Simple Point Charge water model is a re-parametrization of the three-site SPC water model. The SPC model is rigid, whilst the flexible SPC model is flexible. In the model of Toukan and Rahman, the O-H stretching is made anharmonic and thus the dynamical behavior is well described...
) or in implicit water
Implicit solvation
Implicit solvation is a method of representing solvent as a continuous medium instead of individual “explicit” solvent molecules most often used in molecular dynamics simulations and in other applications of molecular mechanics...
models. Mainly designed to simulate the proteins folding
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
and DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
-ligand
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
complexes
Complex (chemistry)
In chemistry, a coordination complex or metal complex, is an atom or ion , bonded to a surrounding array of molecules or anions, that are in turn known as ligands or complexing agents...
in AMBER
AMBER
AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...
force field
Force field (chemistry)
In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
.
The key features
- 3D molecular graphicsMolecular graphicsMolecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...
- Building and editing chemical structures
- Library of building blocks
- Force FieldsForce field (chemistry)In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
: AMBERAMBERAMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...
94, 96, 99SB, 03; OPLSOPLSThe OPLS force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.-Functional form:The functional form of the OPLS force field is very similar to that of AMBER:... - Geometry optimization
- Molecular dynamicsMolecular dynamicsMolecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...
with multiple time step integrator - Hybrid Monte CarloHybrid Monte CarloIn mathematics and physics, the Hybrid Monte Carlo algorithm, also known as Hamiltonian Monte Carlo, is a Markov chain Monte Carlo method for obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult...
- Replica exchange
- GPU accelerated molecular dynamicsMolecular modeling on GPUMolecular modeling on GPU is the technique of using a graphics processing unit for molecular simulations.In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards include many arithmetic units working in parallel...