Here is a collection of tutorials specifically focused on performing analysis in Amber.
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These tutorials focus on analyzing MD simulations with CPPTRAJ.
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.
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.
By Daniel R. Roe
TUTORAL C2: Analysis of Nucleic Acid Simulations
This tutorial will go over using CPPTRAJ to analyze data from simulation of
a nucleic acid system.
By Thomas E. Cheatham III, Christina Bergonzo & Rodrigo Galindo-Murillo
TUTORAL 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
TUTORAL 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
TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ
This tutorial will cover how to perform hydrogen bond analysis with CPPTRAJ.
By Daniel R. Roe
These tutorials focus on analyzing and visualizing MD simulations with PYTRAJ and NGLView.
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 the 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