Tutorials:

Tutorial 1: First CAMPARI Simulation - Torsional Space Monte Carlo Sampling of a Q_N-Peptide ("Polyglutamine") in Implicit Solvent

Tutorial 2: Doing Science with CAMPARI - Determining the Scaling Exponent for Polypeptides in the Excluded Volume Limit

Tutorial 3: An Advanced Monte Carlo Example - The Helix-Coil Transition in the FS-peptide and the Utilization of Replica Exchange

Tutorial 4: Testing Move Sets - How to Establish Global Balance in a Monte Carlo Move Set

Tutorial 5: Molecular Dynamics and Water Models - Pair Correlation Functions in TIP3P and TIP4P Water

Tutorial 6: Introduction to Polynucleotides - Setting up and Running a Complex Simulation in CAMPARI

Tutorial 7: Advanced Simulation Methodology - Calculating the Free Energy of Solvation of Methanol in Water

Tutorial 8: A Technical Introduction to Minimizers in Rigid-Body / Torsional Space

Tutorial 9: Using Umbrella Sampling to Assess the Ability of Polyglutamine (Q₃₀) to Access Conformations with High β-Content

Tutorial 10: Utilizing CAMPARI to Analyze Trajectory Data

Tutorial 11: Structural Clustering and Related Methods in CAMPARI

Tutorial 12: Simulations of Systems Containing Entities Not Supported Natively by CAMPARI

Tutorial 13: The Creation of Toy Models, Energy Landscape Sculpting, and Progress Index-Guided Sampling

Tutorial 14: What You Did Not Know You Could Do with CAMPARI - Part I: The NetCDF Analysis Mode for General Time Series

Tutorial 15: What You Did Not Know You Could Do with CAMPARI - Part II: Molecular Tangram

Tutorial 16: Small Molecule Screens for Computational Docking

Tutorial 17: Utilizing CAMPARI to Process Trajectories from Other Software Like GROMACS

Tutorial 18: Writing Your Own Analyses Through the Python Interface

Tutorial 19: Understanding Advanced Analyses of Kinetic Networks (Markov State Models)

Disclaimer

Note that these tutorials generally imply the use of at least version 3 of CAMPARI. Tutorials 15-16 explicitly rely on version 4. Tutorials 17-19 explicitly rely on version 5. Some of the earlier tutorials can easily be adopted for or even run without changes on earlier versions, but we do not recommend using outdated versions.