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: 100

- 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.