The training will consist of two sessions and participants are expected to attend both of them:
- Wednesday 9th March 2022
- Thursday 10th March 2022
Time: 8:30 – 11:00 GMT / 9:30 – 12:00 CET
Registrant capacity: 30 participants
Each session includes an introduction lecture followed by a tutorial. The trainers are available for one hour in the afternoon if anyone has specific questions about the morning session. This is an interactive course that is presented remotely using Zoom.
Overview: Are you interested in computing free energy using alchemical transformations? Here we give an introduction to free energy calculation in GROMACS. In this course, we focus on two methods to calculate the free energy associated with an alchemical transformation: Bennett acceptance ratio method (BAR) and accelerated weighted histogram (AWH). The tutorials are implemented in Jupyter notebook and cover how to perform a simple alchemical transformation and compute the associated free energy change (e.i solvation free energy) using the two approaches in GROMACS
Audience: These sessions are aimed at people interested in:
1) Starting to compute free energy using GROMACS.
2) Understanding the difference between the approaches available in GROMACS for alchemical transformation.
Pre-requisites: A minimum knowledge of thermodynamics and minimum expertise in using GROMACS to perform Molecular Dynamics calculation are needed to attend the training. Moreover, minimum Linux skills are also required. Please consult the following materials, if you’re uncertain of your Linux, GROMACS and Jupyter notebook skills:
- GROMACS tutorial on Introduction to Molecular Dynamics
- Linux commands, bash shell, a quiz and a link to intro course
- A short guide to Jupyter Notebook
Technical requirements: To participate in the online interactive sessions:
- We recommend using the Zoom desktop app.
- A microphone and (ideally) a webcam.
Note: Technical instructions for the course will be sent out after registration
Learning outcomes: At the end of these sessions, you will be able to
- describe the principles behind Bennett acceptance ratio (BAR) and accelerated weighted histogram (AWH) methods to calculate the free energy difference associated with an alchemical transformation.
- set up and perform simple alchemical transformations using GROMACS
- explain which approach you can apply to your research problem
Trainers: Alessandra Villa, Berk Hess and Sebastian Wingbermühle (KTH – Royal Institute of Technology – Sweden)
Application process: Contact Victoria Hill (firstname.lastname@example.org) explaining briefly:
- how you meet the pre-requisites for the course
- why you want to attend the course and how you will use what you learn in your research project.
We will review applications on a rolling basis to select suitable candidates until the 30 places are filled. The registration instructions to selected participants will be sent by 21 February.
09 Mar, 2022 - 10 Mar, 2022
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