ABOUT THIS EVENT
Molecular Dynamic (MD) simulations are fundamental to understand the mechanism of biological systems. This workshop aims to provide an introduction on the use and on the features of a well-established and highly used package in the field GROMACS.
The workshop covers an introduction to MD simulation, to accelerated weight histogram methods and to GraphicsGraphical Processing Units (GPU) performance. At the end the participants will be familiar with the features of GROMACS code, and they will be able to set up and perform molecular simulation on the covered topic.
PROGRAMME
Thursday, 9 September
9:00-9:05 BioExcel Introduction
Rossen Apostolov
9:05-10:00 Introduction to MD using GROMACS
Alessandra Villa
10:00-10:15 Break
10:15-11:45 Tutorial: Basic MD tutorial
Alessandra Villa
11:45-12:00 Break
12:00-13:00 GROMACS features
Joe Jordan
13:00-14:30 Lunch Break
14:30-15:30 Accelerated Weight Histogram lecture
Berk Hess
15:30-16:30 How to deal with pH effects in GROMACS: from simple peptides to membrane proteins
Miguel Machuqueiro
Friday, 10 September
9:00-11:00 GROMACS GPU performance
Mark Abraham
11:00-11:30 Break
11:30-13:00 DNA base flipping - AWH tutorial
Joe Jordan
13:00-14:30 Lunch Break
14:30-15:00 Rooms with Q&A on GROMACS
15:00-15:30 Watching viral fusion peptides in action: How viruses force their way through the host membrane
Diana Lousa
15.30-16:00 G-Protein Coupled Receptors: the role of molecular dynamics to understand structure-function relationship
Irina Moreira