4 Trajectory Analysis
Analysis of the data is the most time-consuming component of simulation studies. The CPPTRAJ module is 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
4.5 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.
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