Mini-Workshop on Molecular Dynamics (MD) Simulations
September 11-13, 2023 # Medical University of Graz # Austria
Organizer
Laboratory of Computer-Aided Molecular Design, Division of Medicinal Chemistry, Medical University of Graz
About
Access to structural models of biomolecules such as enzymes and proteins has increased enormously in recent years. Together with the elucidation of experimental structures by X-ray crystallography, cryo-electron microscopy and NMR, novel algorithms such as AlphaFold or RFDiffusion have pushed the wave.
In this mini-workshop we will focus on getting hands-on molecular dynamics (MD) simulations, the main technique for exploring the chemical dynamics of biological systems. This workshop is aimed at PhD students who want to learn about MD simulations from scratch: from setting up a system to analysing trajectories. We will focus on two software: Amber and Gromos. There will also be two talks on NMR and Rosetta+AlphaFold by invited speakers.
Details
Schedule
| Monday 11.09.2023 | Tuesday 12.09.2023 | Wednesday 13.09.2023 |
| 10:00-13:00 h CompcAT_hub satellite meeting Accelerating the discovery-to-application path in (bio)catalysis using computational methods | 09:00 – 10:45 h Lecture II “Structure prediction using Rosetta and AlphaFold2“ Horst Lechner 10:45 h Coffe break 11:00 – 13:00 h Lecture III “Force fields and Molecular Dynamics Simulations“ Pedro A. Sánchez Murcia | 09:00 – 10:45 h Practical session II Hands on Amber II: simulation and analysis Data Pedro A. Sánchez Murcia 10:45 h Coffee break 11:00 – 13:00 h Lecture V Introduction to molecular modeling with Gromos Edgar Galicia https://boku.ac.at/en/boku-it/themen/get-connected/bokunet-wlan-pc-raeume/vpn/vpn-with-anyconnect http://mms-teaching.boku.ac.at/jhub/ |
| 13:00 h Lunch | 13:00 h Lunch | |
| 16:00 h Welcome Pedro A. Sanchez Murcia, Vaclav Brazda 16:15 – 17:30 h Lecture I “Dancing Molecules: NMR Insights into Molecular Dynamics” Tobias Madl | 14:00-15:00 h Lecture IV “Main steps in MD simulations” Bruno Di Geronimo 15:00-17:00 h Practical session I Structural databases and molecular viewers Hands on Amber I: setting up, leap Bruno Di Geronimo | 14:00-17:00 h Practical session III Hands on Gromos Edgar Galicia 17:15 h Closing |
| 17:45 h Pizza and beers |
Speakers
Tobias Madl
Medical University of Graz
Horst Lechner
Graz University of Technology
Edgar Galicia
BOKU University of Vienna
Bruno Di Geronimo
Medical University of Graz
Pedro A. Sánchez Murcia
Medical University of Graz
Contact
If you are PhD student and want to participate in the mini-workshop, please write to pedro.murcia(at)medunigraz.at. We have a limited number of places.
CAMDgraz 