[gmx-users] MD Simulations with GROMACS/NAMD/AMBER/VMD: Seasonal School in Stockholm 10-13 June
rossen at kth.se
Sat Apr 27 11:10:31 CEST 2019
The second edition of the BioExcel/PRACE seasonal school in Stockholm is
open for registration, don't miss it!
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 <https://bioexcel.eu/>, 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*
<http://www.gromacs.org/>*, **AMBER* <http://ambermd.org/>*, **NAMD*
<http://www.ks.uiuc.edu/Research/namd/>* and **VMD*
<http://www.ks.uiuc.edu/Research/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
The 2019 Seasonal School is funded and organized jointly with PRACE
<http://www.prace-ri.eu/>, the main HPC resource provider in Europe. The
school is also supported by the Swedish National Infrastructure for
Computing (SNIC) <http://www.snic.se/>. 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
<https://bioexcel.eu/events/bioexcel-spring-school-2017/> 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 <http://pdc.kth.se/> at KTH Royal
Institute of Technology <http://kth.se/> 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.
Please note that the number of places is limited, so register early to
ensure a place.
Additionally, BioExcel CoE will be providing a limited number of travel
bursaries for a fixed amount (€120 per day of the course) for this
event. If you would like to be considered for a travel bursary, please
contact Michelle Mendoca <mailto:mmendonca at ebi.ac.uk>. Please note that
the travel grants will be awarded on a competitive basis and additional
documentation, such as a letter of support and a biography, will be
requested during the application process. More details about the travel
bursary can be found here
REGISTER HERE: https://events.prace-ri.eu/event/868/registrations/605/
We’re looking forward to see you in Stockholm!
Tom Cheatham, Joao Ribeiro, John Stone, Berk Hess, Erik Lindahl
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