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4 Trajectory Analysis

This page contains tutorials on CPPTRAJ, the analysis engine of AmberTools. Please also see Amber-Hub, an online CPPTRAJ manual and tutorials website.

4.1 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

4.2 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

4.3 Analysis of Nucleic Acid Simulations

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

4.4 Introduction to Principal Component Analysis with CPPTRAJ

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

4.5 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.

4.6 Hydrogen Bond Analysis with CPPTRAJ

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

By Daniel R. Roe

"How's that for maxed out?"

Last modified: Mar 24, 2021