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

Requirements for the lectures

- Basic knowledge of biophysics.

Requirements for the tutorials

The tutorials will be provided as an interactive Jupyter notebook based on GROMACS. To be able to follow the tutorials you need to have a basic knowledge of:

- Linux command line.

If you do not have prior experience with this, or if you would like a refresher, please look through this tutorial.

- Jupyter notebook.

Jupyter notebooks are built on Python. If you do not have prior experience with this, or if you would like a refresher, please look through a brief introduction to Jupyter notebook.

Registration

- Free with access to all talks and networking.

- Maximum number of participants: 50.

(registration will be on a first come, first serve basis)

The conference will be provided via Zoom. Registrants will be able to follow the talks via live-stream and will also be able to communicate with speakers and other attendees via direct message. Detailed instructions on virtual platform access will be sent to all registered attendees closer to the date.

Local Organization: Laboratory for Advanced Computing of the University of Coimbra; Centre for Neuroscience and Cell Biology of the University of Coimbra.

The BioData.pt Code of Conduct has been adapted from ELIXIR Hub Code of Conduct for Events so all participants at BioData.pt events can interact with each other in a respectful and safe environment safeguarding their personal integrity in case they believe there has been a breach to this Code of Conduct.

Please note that the event will be recorded.