Getting started

• Installing SAMSON
• Quick Start Guide
• The SAMSON User Guide

SAMSON Tutorials

• Producing publication-quality images
• Snapping, cloning and extracting with selection editors
• Simulating small molecules, graphene and proteins

SAMSON Elements Tutorials

• Building nanotubes models with SAMSON
• Aligning sequences with MUSCLE – Interactive Ramachandran plots
• Calculating non-linear normal modes
• Making nano-batarangs (and more)
• Computing axes of symmetry of biological assemblies
• Generating symmetry mates in SAMSON
• Fast geometry optimization with the FIRE minimizer
• Generating crystal models
• Performing Orbital-Free Density Functional Theory calculations
• Using the RDKit – SMILES Manager
• Ligand unbinding pathway search
• Ligand Path Finder
• Protein conformational transition search
• Protein Path Finder
• ARAP interpolation for Protein structures
• Universal Force Field
• Interactive Modeling UFF (IM-UFF)
• Pathlines
• Optimize transition paths with P-NEB
• Export atoms trajectories along paths
• Molecular docking with AutoDock Vina
• Computing normal modes that open a binding site
• Prepare and minimize using GROMACS Wizard Light
• Prepare, minimize, equilibrate and simulate using GROMACS Wizard

Developing SAMSON Elements

• The SAMSON Developer Guide
• Installing the SAMSON SDK
• Generating a SAMSON Element
• Building a SAMSON Element on Windows
• Building a SAMSON Element on MacOS
• Building a SAMSON Element on Linux
• Distributing a SAMSON Element on SAMSON Connect

Developer tutorials

• Programming new apps
• Handling units and dimensional analysis
• Importing data
• Exporting data
• Creating novel visualizations
• Programming new force fields
• Programming new state updaters: Steepest descent
• Programming new state updaters: Monte Carlo
• Integrating external programs
• Cite your research in SAMSON Elements
• Programming a path generator
• Samples