mambo:Algorithm
The algorithm used in a computational method
mambo:Angle
The angle between two atoms
1
1
mambo:Atom
An elementary constituent of matter, made of a nucleus and electrons
mambo:Barostat
A method for coupling the particles in a molecular dynamics simulation to an external barostat for controlling pressure
mambo:Bond
mambo:BondedPotential
The bonded terms of an interaction potential in simulations
mambo:CartesianCoordinates
The cartesian coordinates of an object in 3D space with respect to a reference system
mambo:ChemicalProperty
A chemical property of a material
mambo:ComputationalMethod
A specific computational method for simulating the properties or the behavior of a material or materials
mambo:Coordinates
The spatial coordinates of a structural entity
mambo:Crystal
A material structure with periodicity in space in one, two or three dimensions
mambo:DFT
A computational method for evaluating interaction potentials based on density functional theory
mambo:Dihedral
mambo:ElectricalMethod
An electrical experimental method or procedure
mambo:ElectroMagneticProperty
An electromagnetic property of a material
mambo:Experiment
An experimental operation/procedure or a set of experimental operations/procedures for determining or measuring the properties or the behavior of a material or materials
mambo:ExperimentalMethod
A specific experimental method for determining or measuring the properties or the behavior of a material or materials
mambo:ExternalCoupling
A method used to couple particles in a molecular dynamics simulation to an external reference systems
mambo:FourBody
A 4-body interaction potential term
mambo:HarteeFock
A computational method for evaluating interaction potentials based on the Hartree-Fock theory
mambo:Integrator
The integrator of the equation of motions in molecular dynamics simulations
mambo:InteractionPotential
The interaction potential used in a specific computational method
mambo:LatticeParameters
The parameters of a lattice in a periodic structure
mambo:Material
A portion of physical matter
mambo:MechanicalProperty
A mechanical property of a material
mambo:MolecularAggregate
A material composed of aggregates of molecules of the same kind or of different kind
mambo:MolecularDynamics
A computational tool or algorithm for molecular dynamics simulation
mambo:MolecularMechanics
A potential based on molecular mechanics
mambo:MolecularSystem
A chemically well-defined system made up of atoms kept together by chemical bonds
mambo:NPT
The constant-pressure constant-temperature (isothermal-isobaric) simulation ensemble in molecular dynamics
mambo:NVE
The constant-energy (microcanonical) simulation ensemble in molecular dynamics
mambo:NVT
The constant-temperature (canonical) simulation ensemble in molecular dynamics
mambo:NonBondedPotential
The non bonded terms of an interaction potential in simulations
mambo:OpticalMethod
An optical experimental method or procedure
mambo:Optimizer
A computational tool or algorithm for structural optimization
mambo:Orientation
The orientation of a system in 3D space with respect to a reference orientation
mambo:Particle
A pseudo-particle used in simulations
mambo:PotentialComponents
The components of an interaction potentials
1
1
mambo:Property
A chemico-physical property of a material or materials
mambo:QuantumMechanics
A potential based on quantum mechanics
mambo:Quaternion
The quaternion coordinate vector of a system in 3D space with respect to a reference orientation
mambo:RotationMatrix
The matrix representing the rotation of a system in 3D space with respect to a reference orientation
mambo:Simulation
A computational operation/procedure or a set of computational operations/procedures for simulating the properties or the behavior of a material or materials
mambo:SimulationEnsembles
The thermodynamic ensemble in which a molecular dynamics simulation is performed
mambo:SphericalCoordinates
The spherical coordinates of an object in 3D space with respect to a reference system
mambo:StructuralEntity
A structural unit in which a structure can be decomposed into
mambo:StructuralUnit
A chemically well-defined structural unit, for example a functional group, constituting
mambo:Structure
The structure of a material or materials
mambo:StructureManipulation
An algorithm or tool for the manipulation of a structure
mambo:TOF
A time-of-flight experimental method
mambo:Thermostat
A method for coupling the particles in a molecular dynamics simulation to an external thermostat for controlling temperature
mambo:ThreeBody
A 3-body interaction potential term
mambo:TopologicalEntities
mambo:TwoBody
A 2-body interaction potential term
BFO:0000002
continuant
BFO:0000002
BFO:0000015
process
BFO:0000015
BFO:0000140
continuant fiat boundary
BFO:0000140
1
H
1.0
1.0
1.0
0.1
0.1
1.0
1
H
2.0
2.0
2.0
0.2
0.2
1.0
1
H
11.0
11.0
11.0
1
H
12.0
12.0
12.0
8
O
0.0
0.0
0.0
0.0
0.0
1.0
8
O
10.0
10.0
10.0
Solvent
2
0.5
0.5
0.5