The laboratory’s teaching activities in molecular simulations focus on computational methods for the study of molecular systems, including molecular dynamics, solvation effects, binding energy estimation, trajectory analysis and enzymatic reaction mechanisms. These activities combine theoretical introduction with guided practical work, and introduce participants to both classical simulation engines and tools for visualization, statistical analysis and interpretation of molecular behaviour.
Topics typically covered include the concepts underlying molecular dynamics simulations and potential energy surfaces, the preparation and execution of simulations, free energy methods such as linear interaction energy and thermodynamic cycles, and practical strategies for analysing results. Complementary techniques, such as multiple sequence alignment and statistical graphics, are used where relevant to support interpretation of simulation outcomes. Teaching materials and workflows are made openly available to facilitate reproducibility and reuse.
Software and Tools Used
- NAMD — Molecular dynamics engine used for production simulations.
- VMD — Visualization program linked to NAMD.
- Chimera — Visualization and molecular graphics.
- R — Statistical analysis software.
- Gnuplot — Graphics and plotting utility.
- ADUN — Framework for solvation and binding energy estimation methods.
- MOLARIS — Advanced energy algorithms, including thermodynamic cycles and EVB.
Courses and Resources
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Concepción, Chile, 01/2026: Course on Molecular Dynamics and Trajectory Analysis — practical introduction combining short lectures with guided sessions; materials and examples available at
https://biocomputing-teaching.github.io/Curso-MD-Analisis/. -
Molecular Simulations (historical course archive) — part of the laboratory’s teaching activities with materials and software linked from the lab portal at
https://mon.uvic.cat/cbbl/teaching/, including references to past molecular simulations content such as potential energy surfaces, Monte Carlo, molecular dynamics and free energy simulations. :contentReference[oaicite:0]{index=0} -
GitHub repository for molecular simulations materials — source code, notebooks and web content related to course workflows can be accessed at
https://github.com/Biocomputing-Teaching/Curso-MD-Analisis.
The combination of simulation engines, visualization tools, statistical and sequence analysis utilities provides a cohesive set of methods for participants to explore both the technical and conceptual aspects of molecular simulations.
The laboratory is also open to contributing to teaching activities in other academic programs, providing course material, practical sessions, or specialized modules related to molecular simulations and computational biophysics.