Online Course on Simulation of Biological Systems 

In this course the different computational chemistry methods which are commonly employed for the simulation of biological processes will be explained during the theoretical lectures (12 hours), including classical molecular dynamics, enhanced-sampling methods, and hybrid quantum mechanics/molecular mechanics (QM/MM) schemes. In addition, during the computer exercises (16 hours) we will model different biological processes with free software: AmberTools, Orca, VMD, MoBioTools, WHAM.

The course will be broadcasted live on our YouTube channel (see links below), where you can participate in the chat. 

Theory Lectures 14:00 – 17:00 GMT+1:00 Madrid

• Day 1. 1st Feb 2022. Molecular Dynamics, Equations of Motion and Force Fields

• Day 2. 4th Feb 2022. Periodic Boundary Conditions. Introduction to Enhanced-Sampling Approaches

• Day 3. 8th Feb 2022. Umbrella Sampling and Replica Exchange

• Day 4. 11th Feb 2022. QM/MM and Research Examples

Computer Exercises 13:00 – 17:00 GMT+1:00 Madrid, Software: AmberTools, Orca, VMD, MoBioTools and WHAM

• Day 5. 15th Feb 2022. Classical Molecular Dynamics

PDF Tutorial

• Day 6. 18th Feb 2022. Umbrella Sampling

PDF Tutorial

• Day 7. 22nd Feb 2022. Computation of Redox Potentials

PDF Tutorial

• Day 8. 25th Feb 2022. Computation of Absorption Spectra

PDF Tutorial

• Day 5. 15th Feb 2022. Classical Molecular Dynamics

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