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Trajectory Analysis

This page contains tutorials on both the CPPTRAJ and PYTRAJ programs, as listed on the index page.

TUTORIAL C0: An Introduction to CPPTRAJ

This tutorial will give a basic introduction to using CPPTRAJ for performing trajectory analysis. It will cover using CPPTRAJ interactively and in batch mode for processing scripts, loading topologies and trajectories, processing data, and working with data sets. (Japanese translation)

By Daniel R. Roe

TUTORIAL C1: RMSD Analysis in CPPTRAJ

This tutorial will give a basic introduction to performing RMSD calculations with CPPTRAJ. It will cover loading reference structures, as well as calculating RMSD to references with different topologies. (Japanese translation )

By Daniel R. Roe

TUTORIAL C2: Analysis of Nucleic Acid Simulations

This tutorial will go over using CPPTRAJ to analyze data from a simulation of a nucleic acid system.

By Thomas E. Cheatham III, Christina Bergonzo & Rodrigo Galindo-Murillo

TUTORIAL C3: Introduction to Principal Component Analysis with CPPTRAJ

This tutorial will go over using CPPTRAJ to perform principal component analysis in Cartesian space.

By Thomas E. Cheatham III, Daniel R. Roe & Rodrigo Galindo-Murillo

TUTORIAL C4: Combined Clustering Analysis with CPPTRAJ

This tutorial will cover how to perform combined clustering analysis with CPPTRAJ, which is a way of comparing structure populations between two or more independent trajectories or between different parts of a single trajectory.

By Daniel R. Roe

TUTORIAL C5: Hydrogen Bond Analysis with CPPTRAJ

This tutorial will cover how to perform hydrogen bond analysis with CPPTRAJ.

By Daniel R. Roe

TUTORIAL P0: An Introduction to PYTRAJ

This tutorial will give a basic introduction to using PYTRAJ for performing trajectory analysis in Jupyter notebook.

By Hai Nguyen

TUTORIAL P1: Simulating Crystals with AMBER Molecular Dynamics - Jupyter notebook version

This tutorial combines Jupyter notebok, PYTRAJ and protein viewer and other packages in AMBER for seting up system for crystal simulation.

By Hai Nguyen

TUTORIAL P2: Using Jupyter notebook remotely

This tutorial will guide you how to use Jupyter notebook remotely.

By Hai Nguyen

TUTORIAL P3: Using NGLView for protein visualization in Jupyter notebook

This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to use pytraj to perform data analysis.

By Hai Nguyen

TUTORIAL P4: Trajectory rendering and movie making with NGLView

This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to quickly make a movie for presentation.

By Hai Nguyen

TUTORIAL P5: Real time molecular dynamics simulation and visualization

This tutorial will guide you how to use AmberTools and NGLView to perform molecular dynamics simulation and visualize the trajectory in real time.

By Hai Nguyen

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Last modified: Jan 29, 2018