Abalone is a general purpose
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the ...
and
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". Ever since Dalton's atoms and KekulĂ ...
program for simulations of bio-molecules in a
periodic boundary conditions
Periodic boundary conditions (PBCs) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a ''unit cell''. PBCs are often used in computer simulations and mathematical mode ...
in explicit (
flexible SPC water model
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water (molecule), water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular m ...
) or in
implicit water models. Mainly designed to simulate the
protein folding
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproduci ...
and
DNA-
ligand
In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electr ...
complexes in
AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In Ma ...
force field.
Key features
* 3D
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". Ever since Dalton's atoms and KekulĂ ...
Automatic Force Field generator for bioelements: H, C, N, O* Building and
editing chemical structures
* Library of building blocks
*
Force fields
Force field may refer to:
Science
* Force field (chemistry), a set of parameter and equations for use in molecular mechanics simulations
* Force field (physics), a vector field indicating the forces exerted by one object on another
* Force field ( ...
: Assisted Model Building with Energy Refinement (
AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In Ma ...
) 94, 96, 99SB, 03; Optimized Potentials for Liquid Simulations (
OPLS
The OPLS (Optimized Potentials for Liquid Simulations) 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 tha ...
)
* Geometry optimizing
*
Molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the ...
with multiple time step integrator
*
Hybrid Monte Carlo The Hamiltonian Monte Carlo algorithm (originally known as hybrid Monte Carlo) is a Markov chain Monte Carlo method for obtaining a sequence of random samples which converge to being distributed according to a target probability distribution for whi ...
*
Replica exchange
Parallel tempering in physics and statistics, is a computer simulation method typically used to find the lowest free energy state of a system of many interacting particles at low temperature. That is, the one expected to be observed in reality. ...
* Interface with quantum chemistry -
ORCA
The orca or killer whale (''Orcinus orca'') is a toothed whale belonging to the oceanic dolphin family, of which it is the largest member. It is the only Extant taxon, extant species in the genus ''Orcinus'' and is recognizable by its black ...
,
NWChem
NWChem is an ab initio computational chemistry software package which includes quantum chemical and molecular dynamics functionality.
It was designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. ...
,
Firefly
The Lampyridae are a family of elateroid beetles with more than 2,000 described species, many of which are light-emitting. They are soft-bodied beetles commonly called fireflies, lightning bugs, or glowworms for their conspicuous production ...
(PC GAMESS),
CP2K
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provi ...
*
GPU accelerated molecular modeling
See also
References
External links
*
Benchmarking
{{DEFAULTSORT:Abalone (Molecular Mechanics)
Monte Carlo software
Computational chemistry software
Molecular dynamics software
Molecular modelling software
Science software