AmberTutorials
Contents
Modular Tutorials
Workshop Materials
Internal guides
In Progress Tutorials
Training a QM/MM+ΔMLP model with DeePMD-kit from AMBER simulation data
Learning to Run Absolute Binding Free Energy Calculations
Optimizing Lambda Schedules for Alchemical Free Energy Calculations
VMD Basics for Visualization
CPPTRAJ for Analysis
Learning Objectives
Tutorial
TCL Scripting Basics
Writing a VMD TCL Script
Alchemical free energy calculations of pKa shifts in the MTR1 ribozyme
AmberTutorials
In Progress Tutorials
CPPTRAJ for Analysis
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CPPTRAJ for Analysis
Lauren Lerew
1
and Darrin M. York
1
1
Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
Learning Objectives
Tutorial