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  • Docs
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  • Contents
  • HTMD
    • Installation
    • Tutorials
      • Introduction to HTMD
        • Python primer
        • Getting started with HTMD
        • HTMD Molecules
        • Visualization in HTMD
      • Building with HTMD
        • Protein preparation
        • Advanced building
        • System building protein-ligand
        • System building protein in Membrane
      • Simulations in HTMD
        • Molecular Dynamics in HTMD
        • Adaptive Sampling Explained
        • Adaptive Sampling Tutorial
        • Adaptive Bandit Tutorial
      • Analysis in HTMD
        • Getting Started with Projections
        • Ligand binding analysis
        • Protein folding analysis
        • CXCL12 conformational analysis
      • Advanced uses
        • System building Protein-Protein
        • Using docking to initialize positions
        • Equilibration protocol for the mu opioid GPCR
      • Tools
        • Maximal Substructural Alignment
        • Sequence Based Alignment
        • FFEvaluate
        • Membrane Builder
      • Changelog
        • 1.12.0 (stable) - 2018/03/22
        • 1.10.0 (stable) - 2017/10/25
        • 1.8.0 (stable) - 2017/07/17
        • 1.6.0 (stable) - 2017/03/01
    • Documentation
      • Molecule
      • Building
        • Solvating
        • Protein preparation
        • CHARMM builder
        • AMBER builder
      • MD Simulations
        • Applications
        • Adaptive sampling
        • State-of-the-art protocols for molecular simulations
      • Simulation List
      • Projections
        • MetricData - Storage for projected data
        • Metric - Helper class for combining Metrics for projection
        • MetricCoordinate - coordinates of an atom selection
        • MetricDistance - (Self-)distance-based metrics between atoms selections
        • MetricDihedral - Dihedral-based metrics
        • MetricRmsd - RMSD-based metric
        • MetricShell - occupancy of an atom selection (e.g. water) around another selection
        • MetricSecondaryStructure - secondary structure-based metric
        • MetricPlumed2 - access all Plumed2 metrics (CVs)
        • MetricSasa - Solvent accessible surface area
        • MetricTMscore - TMscore-based metric
        • MetricFluctuation - RMSF-based metric
      • Dimensionality Reduction
        • TICA - Time independent component analysis
        • KMeansTri - kmeans triangle inequality
        • GWPCA Principal Component Analysis
      • Clustering
        • KCenters clustering method
        • RegCluster regular sized clustering
      • Markov state models
      • Kinetics
    • API
      • Subpackages
        • htmd.adaptive package
        • htmd.apps package
        • htmd.builder package
        • htmd.clustering package
        • htmd.membranebuilder package
        • htmd.molecule package
        • htmd.projections package
        • htmd.protocols package
        • htmd.queues package
      • Submodules
        • htmd.config module
        • htmd.decorators module
        • htmd.dock module
        • htmd.home module
        • htmd.kinetics module
        • htmd.kineticshmm module
        • htmd.latest module
        • htmd.metricdata module
        • htmd.model module
        • htmd.modelhmm module
        • htmd.mutualinformation module
        • htmd.numbautil module
        • htmd.parallelprogress module
        • htmd.pathplanning module
        • htmd.session module
        • htmd.simlist module
        • htmd.ui module
        • htmd.units module
        • htmd.util module
        • htmd.version module
        • htmd.versionwarnings module
      • Module contents
    • Developer’s Guide
      • How to contribute
        • Introduction
        • How to Contribute Fixes
        • How to Contribute New Features
        • Contributor Agreement
        • List of Features Interesting for HTMD
      • Guidelines for developers
        • Coding Style Tips
        • Using modules inside HTMD
        • Using Docstrings and Doctests
      • Versioning
        • HTMD Versions Explained
        • How to release a new HTMD version?
  • Moleculekit
    • Installation
      • Downloading miniconda
      • Create a conda environment
      • Install with pip
      • Install with conda
    • The Molecule class
    • The SmallMol class
    • Molecule tools
      • Contents
        • Protein segmentation: Automatically detects and assigns segments in proteins
        • Protein preparation: Protonates proteins and optimizes hbond networks
        • Sequence-based structure alignment: Aligns two protein structures by their sequence alignment
        • Voxel Descriptors: Calculates 3D voxels channels containing features of a Molecule or SmallMol
        • Maximal substructure alignment: Aligns two small molecules by their maximal substructure
    • Projections
      • Contents
        • MetricCoordinate: xyz coordinate projection
        • MetricDihedral: dihedral angles projection
        • MetricDistance: atom distances/contacts projection
        • MetricFluctuation: atom position fluctuations
        • MetricPlumed2: support for Plumed2 projections
        • MetricRmsd: root mean square deviation of structures to a reference
        • MetricSasa: solvent accessible surface area projection
        • MetricSecondaryStructure: protein secondary structure projection
        • MetricShell: density of atoms in shells around other atoms
        • MetricSphericalCoordinate: spherical coordinates of two COMs
        • MetricTMscore: TMscore projection
    • Tutorials
      • Contents
        • Voxelization
  • ACEMD v3
    • Capabilities
      • Not available capabilities
    • Performance
      • Speed benchmarks
    • Release notes
      • 3.2.4 (2020-04-23)
      • 3.2.3 (2019-11-12)
      • 3.2.2 (2019-10-08)
      • 3.2.1 (2019-09-20)
      • 3.2.0 (2019-08-27)
      • 3.1.2 (2019-06-04)
      • 3.1.1 (2019-05-08)
      • 3.1.0 (2019-04-18)
      • 3.0.4 (2019-02-27)
      • 3.0.3 (2019-02-25)
      • 3.0.2 (2018-03-28)
      • 3.0.1 (2017-12-18)
      • 3.0.0 (2017-12-12)
    • Installation
      • Dependencies
    • Tutorial
      • Molecular dynamics simulation of DHFR
      • Migrating from the old ACEMD
    • Reference
      • Command line arguments
      • Input file options
        • Force field
        • Iteractions
        • Restraints
        • Initial state
        • Minimization
        • Integrator
        • Thermostat
        • Barostat
        • Output
    • Licence
    • Support
  • ACEMD v2 (deprecated)
    • ACEMD Manual
      • Introduction
        • Fundamental units
        • Force field parameters
      • Running ACEMD
        • Specifying an Input File
        • Command Help
        • Selecting a GPU
        • Running parallel ensembles
      • Simulation Configuration
        • Quick Configurations
        • NVT vs NPT ensemble
        • Input Files
        • Output Files
        • Standard output
        • Restarting
      • Advanced material
        • Tcl Scripting
        • Debug TCL scripts
        • PLUMED library
        • Plugin interface
        • Getting support
      • Citations
    • ACEMD Command Reference
      • Configuration
      • Input
      • Output
      • Forcefield
      • Charmm
      • Amber
      • Martini
      • Electrostatics
      • Barostat
      • Thermostat
      • Constraints
      • External Forces
      • Minimisation
      • Interactive
      • Extensions
      • TCL Extension
      • Analysis
  • Parameterize
    • Method
    • Tutorial
      • Prepare molecule
      • Get command-line options
        • Positional Arguments
        • Named Arguments
      • Set total charge
      • Choose force field
      • Atomic charges
      • List parameterizable dihedral angles
      • Choose QM code
      • Choose QM level
      • Control the execution of QM calculations
      • Reuse QM and re-parametrize
      • Find and validate parameters
    • Usage
      • Positional Arguments
      • Named Arguments
 
  • Docs »
  • HTMD »
  • Tutorials »
  • Simulations in HTMD

Simulations in HTMD¶

Contents:

  • Molecular Dynamics in HTMD
  • Adaptive Sampling Explained
  • Adaptive Sampling Tutorial
  • Adaptive Bandit Tutorial
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