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

Rossen Apostolov rossen at kth.se
Sat Apr 27 11:10:31 CEST 2019

Hi everyone,

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 
use them!

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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