Meterials for students
Materials for the course "Basics of Molecular Simulations" taught at the Charles University, Prague.
Course codes: NBCM051 (MFF UK) & MC260P79 (PřF UK)
Lecturs (winter semester 2017/2018): each Wednesday, 10:40am, Ke Karlovu 3, Praha 2, Seminarni mistnost KCHFO (suteren).
MD Lab exercises: December (exact dates to be announced) , Ke Karlovu 3, room M-145 (36) (suteren). For MD lab materials, see below.
This course is best suited for master and doctoral students at MFF and PřF UK
It is practically-oriented, topics range from physical chemistry to biophysics with the focus on the latter.
The topics include:
- Physical basis of molecular interactions
- Methods and algorithms used in modern molecular MD simulations
- Practical examples of simulations for various biophysical systems
- Data analysis and visualization, including modern Big Data and machine learning techniques
Applications of MD simulations to biological, pharmaceutical, and medical problems will be discussed.
- Localization and action of small drug molecules in cellular membranes
- Drug permeability across membranes
- Drug-protein interactions
- Molecular drug delivery systems
- Ageing - lipids under oxidative stress, apoptosis
- Implants biocompatibility
Lecture notes (individual links will become available during the semester):
- Lecture 1, Introduction: link
- Lecture 2, Force fields: link
- Lecture 3, Integrators: link
- Lecture 4, PBC, cutoffs, PME: link
- Lecture 5, Neighbours, constraints: link
- Lecture 6, Ensembles: link
- Lecture 7, Simulation protocol: link
- Lecture 8, Analysis: link
- Lecture 9, Monte Carlo & Docking: link
MD Lab materials: link
Note! Attending and passing the MD Labs is obligatory in order to pass the course. The MD Labs take place in December 2017 (exact dates to be announced) at Počítačová laboratoř Karlov (link)
Papers for dicussion (individual links will become available during the semester):
- Paper 1: link
- Paper 2: link
- Paper 3: link
- Paper 4: link
- Paper 5: link
- Paper 6: link
- Paper 7: link
- Paper 8: link
Python examples (Jupyter Notebooks):