pytraj 1.0.9
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      • Analysis
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      • Topology
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      • Atom mask selection
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  • Basic examples »
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TutorialsΒΆ

Try pytraj online:

http://mybinder.org/assets/images/logo.svg

If you miss any Python package, try to use conda, example:

conda install seaborn

Basic

  • Basic examples
    • How to run pytraj
    • Load a Topology and Trajectory
    • Select atoms
    • Distance between two COMs
    • DSSP analysis
    • Hbond analysis
    • More examples
  • Energy decomposition with sander and igb8 solvent model
  • Closest solvents
  • Principal component analysis
  • Autoimage
  • Parallel computing tutorial
  • Plots
    • Plot H-bond distances
    • Plot correlation matrix
    • Pairwise RMSD
    • Principal component analysis
    • Ramachandran plot
    • Plot rmsd and radgyr correlation
    • Nucleic acid torsion angle distribution
    • Radial distribution function of waters
    • RMSF
    • Lowest curve plot below data cloud
  • Interface with other packages
    • Interface with mdtraj
    • Interface with mdanalysis
    • Interface with cclib

Advanced

  • Advanced examples
    • Lysozyme NH order parameters
    • Hbond
    • Endless streaming calculation
    • Use Jupyter notebook remotely
  • Data analysis for trp-cage folding MD trajectory
  • Python tricks that make your life easier
  • Cookbook
  • How to run Jupyter notebook

AMBER tutorials

Let's go

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Last updated on Oct 25, 2016.
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