GROMACS Workshop

BioData.pt | ELIXIR Portugal

This event aims to provide an introduction on the use and on the features of a well-established and highly used package in the field GROMACS

<h2>About this event
</h2>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. 
 
<h2>Programme
</h2><h3>Thursday, 9 September 
</h3>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

<h2>Requirements for the lectures</h2>- Basic knowledge of biophysics. <h2>Requirements for the tutorials</h2>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 <a href="https://swcarpentry.github.io/shell-novice/" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">tutorial</a>.- 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 href="https://drive.google.com/file/d/1tgpp0xVDo3WuqMGSBrcjwZ6sdf67gDGQ/view?usp=sharing" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer"> a brief introduction to Jupyter notebook.</a> <h2>Registration</h2>- 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. <h2>Local organization</h2>Laboratory for Advanced Computing of the University of CoimbraCentre for Neuroscience and Cell Biology of the University of Coimbra

<h3>Code of Conduct</h3>The <a href="https://biodata.pt/sites/default/files/2021-02/BioData.pt%20Code%20of%20Conduct%20for%20Events.pdf" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">BioData.pt Code of Conduct</a> 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.

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GROMACS Workshop

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GROMACS Workshop

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