Getting started

• What’s new in SAMSON 2021?
• What’s new in SAMSON 2020 R3?
• What’s new in SAMSON 2020 R2?
• What’s new in SAMSON 2020?
• Installing SAMSON
• Quick Start Guide
• The SAMSON User Guide

SAMSON Tutorials

• Camera: moving around
• Selecting objects
• Moving objects
• Producing publication-quality images
• Inspecting objects
• Simulating small molecules, graphene, and proteins
• Node Specification Language

SAMSON Extensions Tutorials

General

• Export atoms trajectories along paths
• Fast geometry optimization with the FIRE minimizer
• Interactive Modeling Universal Force Field (IM-UFF)
• Atoms Selector and Simple Script: making nano-batarangs (and more)
• Optimize transition paths with P-NEB
• Pathlines: show a path of the center of mass of an atomic system
• Prepare, minimize, equilibrate and simulate using GROMACS Wizard
• Universal Force Field

Structural biology

• Aligning proteins
• Computing axes of symmetry of biological assemblies
• Computing non-linear normal modes
• Computing normal modes that open a binding site
• Covalent and non-covalent protein-ligand docking with the Fitted Suite by Molecular Forecaster
• Docking ligands and ligand libraries with AutoDock Vina Extended
• Generating a path between protein structures
• Generating symmetry mates
• Ligand Path Finder
• Perform Positional Analogue Scanning using the SMILES Manager
• Protein docking with Hex
• Protein Path Finder
• Interactive Ramachandran Plot
• Using the RDKit – SMILES Manager

Materials

• Building carbon nanotube models
• Generating crystal models

DNA origami

• Adenita SAMSON Edition: Interactive 3D modeling and visualization of DNA Nanostructures

Developing SAMSON Extensions

• Object-oriented programming in C++
• The SAMSON Developer Guide
• Installing the SAMSON SDK
• Generating a SAMSON Extension
• Building a SAMSON Extension on Windows
• Building a SAMSON Extension on MacOS
• Building a SAMSON Extension on Linux
• Distributing a SAMSON Extension 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 Extensions
• Programming a path generator
• Samples