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Join us on Friday 10th June for the fourth webinar in BioExcel’s webinar series on  computational methods and applications for biomolecular research. The series cover broad topics related to the latest development of major software packages; their application to modelling and simulation; best practices for performance tuning and efficient usage on HPC and novel architectures; introductory tutorials for novel users and much more.

The webinars include an audience Q&A session during which attendees can ask questions and make suggestions. They are a great opportunity to interact with the main code developers.

The next webinar in the series will be:

Webinar: “Mutation free energy calculations with pmx”
Presenter: Bert de Groot
Date: Friday, June 10, 2016
Time: 16:00-17:00 CET (Central European Time)

Registration: Free – register online at https://attendee.gotowebinar.com/register/7380606316561020163. After registering, you will receive a confirmation email containing information about joining the webinar.

Mutation free energy calculations with pmx

BertBert de Groot

Max Planck Institute for Biophysical Chemistry, Computational biomolecular dynamics group, Am Fassberg 11, 37077 Göttingen, Germany


Abstract: The free energy is a central thermodynamic quantity that determines the direction of spontaneous processes. As such, they define binding affinities (association free energies) or stabilities (folding free energies). The calculation of free energies from molecular dynamics simulations has come of age and nowadays reaches remarkable accuracies, routinely achieving quantitative or semi-quantitative agreement with experimental data.

One important branch of free energy calculations involve alchemical transformations such as the annihilation of particles or the mutation of
amino acids. A challenging aspect of these calculations is the creation of associated molecular topologies. pmx provides an automated framework for the introduction of amino acid mutations in proteins. Several state of the art force fields are supported that can be used in the gromacs molecular dynamics package. An introduction into pmx installation, design and usage will be presented, along with a set of benchmark applications that illustrates its use in the prediction of mutation free energies.

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