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  • acelleralive
  • HOME
  • Documentation
  • Download
  • Workshop
  • Help
  • GitHub
  • Video Tutorials
  • Contents
  • HTMD
    • User Guide
      • 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
      • 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
      • 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
    • HTMD Documentation
      • Molecule
        • Molecule module
      • Building
        • Solvating
        • Protein preparation
        • CHARMM builder
        • AMBER builder
      • MD Simulations
        • Applications
        • Queues
        • 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
      • Molecular viewer
    • 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?
  • ACEMD
    • 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
  • AceCloud
    • How to Setup AceCloud
      • Sign Up to AWS
      • Install the AceCloud Client Software
      • Configuring AceCloud
    • How to Use AceCloud
      • Running simulations
      • Checking simulations progress
      • Retrieving simulations results
    • Important Notes on AWS use
  • Parameterize
    • Method
    • Tutorial
      • Prepare molecule
      • Get command-line options
        • Positional Arguments
        • Named Arguments
      • Set total charge
      • Choose force field
      • 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
  • AceFlow
    • Build Flow
      • Usage
      • Examples
    • SimpleRun Flow
      • Usage
      • Examples
    • RunAdaptLig Flow
      • Usage
      • Examples
    • CheckAdaptLig Flow
      • Usage
      • Example
  • ACEMD3
    • Installing ACEMD3
    • Running ACEMD3
    • Input file changes
    • Discontinued Features
    • Support

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  • Simulations in HTMD

Simulations in HTMD¶

Contents:

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