Practical Course on Molecular Dynamics and Trajectory Analysis
Organization
- Dates: January 15, 16, and 19, 2026
- Location: Universidad Andres Bello, Concepcion, Chile
- Format: In-person, hands-on (morning and afternoon)
- Language: Spanish
- Instructor: Jordi Villa i Freixa, Computational Biochemistry and Biophysics Lab, Universitat de Vic - Universitat Central de Catalunya, IRIS-CC
- Limited spots: 15-20 participants
- Registration required in advance
- Contact: Veronica Andrea Jimenez Curihual veronica.jimenez@unab.cl
Prerequisites
- Basic knowledge of molecular simulations or computational chemistry
- Familiarity with the Linux command line
- Basic Python knowledge
- Access to a GPU cluster or workstation, ideally with OpenMM
Course program
Day 1: Thursday, January 15
Main theme: Fundamentals of classical simulations with OpenMM
Morning (09:00 - 13:00):
- Welcome and course overview
- Minimal theory of molecular dynamics
- System preparation in OpenMM (topology, force field, solvent)
- Parameterization with OpenMM and OpenFF
- Running short GPU simulations
Afternoon (14:30 - 18:00):
- Basic trajectory analysis with MDAnalysis
- Exercises: RMSD, RMSF, radius of gyration, internal distances
- Quality control best practices
Day 2: Friday, January 16
Main theme: Advanced techniques and Markov models
Morning (09:00 - 13:00):
- Advanced techniques in OpenMM:
- Steered MD (SMD)
- Umbrella Sampling
- Metadynamics
- Setup and execution of advanced protocols
- Efficiency and scalability considerations
Afternoon (14:30 - 18:00):
- Markov models with PyEMMA
- MSM introduction
- Feature extraction with MDAnalysis + PyEMMA
- Clustering and model construction
- Relaxation times and metastable states
- Applied case: conformational transitions in a protein
Day 3: Monday, January 19 (morning only)
Main theme: Individual projects and consultation
Morning (09:30 - 13:00):
- Participant project discussions
- Personalized technical consultation
- Best-practice recommendations for simulations and analysis
Course talk
Expanded material based on the course beamer, with one HTML chapter per session:
Collaborators
With collaboration from 
. Pan-European Network on Computational Redesign of Enzymes.
Supported by Fondecyt Fondo Nacional de Desarrollo Cientifico y Tecnologico
