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