MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June

From: Joao Ribeiro (
Date: Tue Apr 30 2019 - 09:43:46 CDT

Do you want to learn how to take your simulations to the next level and learn how to make your simulations faster/better, how to use more exotic algorithms, how to exploit ensemble sampling, create stunning illustrations, and not least get a chance to interact and discuss your research with code developers and PIs?


On June 10-13, some of the core developers of NAMD, AMBER, GROMACS and VMD will jointly give a 4-day PRACE seasonal school on advanced molecular simulations hosted by PDC:


Registration is here:



BioExcel, the leading European Center of Excellence for Computational Biomolecular Research, is once again bringing the main developers of some of the most popular and well-known applications for molecular modelling and simulations – GROMACS, AMBER, NAMD and VMD together. Last time we had a great time interacting with lots of skilled students and postdocs, and in particular to talk about challenges for our field that unify the field and codes. We look forward to meeting you this year, both to help you use the tools better and to help us learn from how you would like to use them!


The 2019 Seasonal School is funded and organized jointly with PRACE, the main HPC resource provider in Europe. The school is also supported by the Swedish National Infrastructure for Computing (SNIC). Molecular modelling and simulations are integral part of biomolecular research. Yet, there is insufficient expertise on efficient usage of HPC resources among the user community. The current school is organized to fill that gap and builds on the very successful first edition of the event.

Over the 4 days of the event, the school program will allow participants to get a comprehensive understanding of the usage of the different codes, their scalability and performance, exploiting the strengths of each code while avoiding their weaknesses.


You will both learn the theoretical background and get hands-on experience with how to prepare advanced simulations, how others think about concepts such as force fields and relaxation, how to use free energy calculations, adaptive weight histogramming, replica exchange simulations, various types of GPUs/accelerators, ensemble sampling e.g. with Markov State Models, and how to create jaw-dropping illustrations with ambient occlusion from your simulations. The teaching will be given on a level where we expect the participants to have prior experience with some MD code; while you are welcome to participate no matter what, be aware that we won’t go through a pure introduction to MD simulations.



The course will take place at the computer laboratories of PDC Center for High Performance Computing at KTH Royal Institute of Technology in Stockholm. Participants will be able to run on the PRACE Tier­‐1 system Beskow, the largest Tier-1 system within the Nordic countries.

The program is free of charge but participants are responsible for own travel and accommodation costs. During the hands-on sessions participants can use own laptops, provided that all the required software is installed prior to the event. A detailed list of needed applications will be communicated in advance.

Both academic and industrial researchers residing in PRACE member countries, European Union Member States or Associated Countries, are welcome to apply to attend the school. All lectures and training sessions will be in English--B_3639462226_4528606--

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