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MMTK User Guide 2.7.5 documentation
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MMTK User Guide
¶
MMTK User’s Guide
Introduction
Overview
Using MMTK
Modules
Objects
Chemical objects
Collections
Force fields
Universes
Minimizers and integrators
Trajectories
Variables
Normal modes
Non-MMTK objects
The chemical database
Force fields
Units
A simple example
Constructing a molecular system
Creating chemical objects
Proteins, peptide chains, and nucleotide chains
Lattices
Random numbers
Collections
Creating universes
Force fields
Referring to objects and parts of objects
The structure of peptide and nucleotide chains
Analyzing and modifying atom properties
General operations
Coordinate transformations
Atomic property objects
Configurations
Minimization and Molecular Dynamics
Trajectories
Options for minimization and dynamics
Periodic actions
Fixed atoms
Energy minimization
Molecular dynamics
Velocities
Distance constraints
Thermostats and barostats
Integration
Snapshots
Normal modes
Analysis operations
Properties of chemical objects and universes
Energy evaluation
Surfaces and volumes
Miscellaneous operations
Saving, loading, and copying objects
Exporting to specific file formats and visualization
PDB, VRML, and DCD files
Visualization and animation
Fields
Charge fitting
Constructing the database
Atom definitions
Group definitions
Molecule definitions
Complex definitions
Protein definitions
Threads and parallelization
Bibliography
Glossary
Code examples
¶
Code Examples
Module reference
¶
Module Reference
MMTK
MMTK.Biopolymers
MMTK.Bonds
MMTK.ChargeFit
MMTK.ChemicalObjects
MMTK.Collections
MMTK.ConfigIO
MMTK.DCD
MMTK.Deformation
MMTK.Dynamics
MMTK.Environment
MMTK.Field
MMTK.ForceFields
MMTK.ForceFields.AmberForceField
MMTK.ForceFields.AnisotropicNetworkForceField
MMTK.ForceFields.CalphaForceField
MMTK.ForceFields.DeformationForceField
MMTK.ForceFields.HarmonicForceField
MMTK.ForceFields.LennardJonesForceField
MMTK.ForceFields.SPCEForceField
MMTK.ForceFields.ForceFieldTest
MMTK.ForceFields.Restraints
MMTK.FourierBasis
MMTK.Geometry
MMTK.InternalCoordinates
MMTK.Minimization
MMTK.MolecularSurface
MMTK.MoleculeFactory
MMTK.NormalModes
MMTK.NormalModes.BrownianModes
MMTK.NormalModes.EnergeticModes
MMTK.NormalModes.VibrationalModes
MMTK.NucleicAcids
MMTK.PDB
MMTK.PDBMoleculeFactory
MMTK.ParticleProperties
MMTK.ProteinFriction
MMTK.Proteins
MMTK.Random
MMTK.Solvation
MMTK.Subspace
MMTK.Trajectory
MMTK.Units
MMTK.Universe
MMTK.Visualization
MMTK.XML
Indices and tables
¶
Index
Module Index
Search Page
Table Of Contents
MMTK User Guide
Code examples
Module reference
Indices and tables
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