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.
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.
translation) By Daniel R. Roe.
RMSD Analysis in
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
) By Daniel R. Roe.
Analysis of A Nucleic Acid Simulation
This tutorial will go over using CPPTRAJ to
analyze data from a simulation of a nucleic acid system.
Introduction to Principal Component Analysis with
This tutorial will go over using CPPTRAJ to perform principal
component analysis in Cartesian space.
Combined Clustering Analysis with
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
Hydrogen Bond Analysis with CPPTRAJ
This tutorial will cover how to perform hydrogen bond analysis with
CPPTRAJ. By Daniel R. Roe.
Analysis of MAD2 using PCA, tICA, and Markov State Models
This tutorial will cover the basic theory behind PCA and tICA, and Markov State Models.
It will then apply those concepts to demonstrate their applications in a case study in characterizing secondary structure changes
in the MAD2 protein, a metamorphic protein. By Alberto Perez and Elizabeth Sebastian.