Webinar: COMPSs: a high level framework for the development of parallel applications (2018-11-07)
BioExcel’s webinar series continue with a presentation by Dr. Daniele Lezzi, Barcelona Supercomputing Center. Register Abstract One of the biggest challenges in the programming of scientific application is the efficient exploitation of computing infrastructures. In the era of Big Data applications one of the pressing requirements on the researcher is to achieve a convergence between […]
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Accelerating sampling in GROMACS with the AWH method
Overview Simulation of conformational transitions in bio-molecules is often problematic because transitions occur over timescales that are longer than what can be simulated. If one has a good reaction coordinate, transitions can be accelerated by up to several orders of magnitude by applying a biasing potential. In this webinar we will show how the Accelerated […]
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Webinar: Enhanced molecular simulations with PLUMED (2019-09-12)
BioExcel’s webinar series continue with a presentation by Gareth Tribello Register Abstract PLUMED is a plugin that can be used in tandem with a number of different molecular dynamics codes. The original paper on PLUMED was published 10 years ago and the code has had a success that we could not possibly have envisioned when […]
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Webinar: More bang for your buck: Improved use of GPU Nodes for GROMACS 2018 (2019-09-05)
BioExcel’s webinar series continue with a presentation by Carsten Kutzner Register Abstract We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, […]
Read MoreWebinar: Prediction of protein-protein interactions in CAPRI: an increasingly integrative approach (2019-06-27)
BioExcel’s webinar series continue with a presentation by Shoshana Wodak and Marc Lensink Register Abstract CAPRI (Critical Assessment of PRediction of Interaction) is a community wide experiment designed to test methods to predict the structure of macromolecular complexes based on the known structure of their components (http://www.ebi.ac.uk/msd-srv/capri/). The experiment, inspired by CASP, was started in […]
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Webinar: GROMACS 2019 – overview of the new features and capabilities (2019-05-17)
BioExcel’s webinar series continue with a presentation by Mark Abraham Register Abstract Each new major release of GROMACS brings with it the latest in feature development, hardware support, performance enhancements, and usability improvements. In this webinar we will review and describe the major new changes, and guide you to make best use of the […]
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Webinar: MDBenchmark: a tedious task – made straightforward (2018-11-23)
BioExcel’s webinar series continue with a presentation by Michael Gecht Register Abstract Molecular dynamics software is optimized to yield the highest performance on available resources. The details of why computations perform better or worse depends on various parameters. As an example, common biomolecular simulations stop to scale linearly when too much computational power is provided. […]
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Webinar: COMPSs: a high level framework for the development of parallel applications (2018-11-07)
BioExcel’s webinar series continue with a presentation by Dr. Daniele Lezzi, Barcelona Supercomputing Center. Register Abstract One of the biggest challenges in the programming of scientific application is the efficient exploitation of computing infrastructures. In the era of Big Data applications one of the pressing requirements on the researcher is to achieve a convergence between […]
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Webinar: How to contribute to GROMACS code and documentation: where it is and how to use it (2018-10-30)
BioExcel’s webinar series continue with a presentation by Dr. Paul Bauer, Lindahl group. Register Abstract I’ll give a short overview about how to successfully contribute new content to the GROMACS project, going into detail for contribution policies and our code review and acceptance standards. I’ll explain how to find the necessary information in the GROMACS […]
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Webinar: Open Force Field Initiative: The SMIRNOFF format and learned chemical perception (2018-10-10)
BioExcel’s webinar series continue with a presentation by Caitlin C. Bannan Mobley Group, UC Irvine – Chemistry Department Register Abstract The Open Force Field Initiative (openforcefield.org) is developing a machinery to automatically parameterize molecular mechanics force fields. An important part of this process will be automating chemical perception — the way force field parameters are […]
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