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DTSTAMP:20260705T155411Z
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DTSTART:20210201T080000Z
DTEND:20210203T110000Z
DESCRIPTION:This course will be delivered as an ONLINE EVENT for remote par
 ticipation due to the COVID-19 measures enforced by most European governme
 nts.\n\nDescription\n\nThis course gives a practical introduction on how t
 o run GROMACS MD simulations efficiently on modern hardware including both
  CPUs and GPUs. In addition to speeding up MD simulations\, also workflow 
 automation and advanced sampling techniques are discussed. CSC's Puhti and
  Mahti supercomputers will be used for the hands-on exercises.\n\nThe cour
 se consists of lectures and hands-on exercises. GROMACS will be used in th
 e exercise sessions.\n\nThe event is organized in collaboration with BioEx
 cel and CSC and supported by PRACE.\n\nLearning outcome\n\nAfter the cours
 e the participants should have the skills and knowledge needed to efficien
 tly use CPU and GPU resources in GROMACS simulations.\n\nPrerequisites\n\n
 The participants are assumed to have working knowledge of GROMACS\, basic 
 Python and Linux/Unix skills are required. The fundamentals of molecular d
 ynamics or basic usage of GROMACS are not covered on this course. Please c
 onsult these materials (pdf)\, if you're uncertain of your Python\, Linux 
 or GROMACS skills.\n\nAgenda (NOTE: Times are CET)\n\nDay 1\, Monday 1.2\n
 \n\n	\n	 9:00 – 9:30  Introduction\, organization (TBA)\n	\n	\n	 9:30
  –11:30 QM/MM simulations with GROMACS and CP2K (Dmitry Morozov)\n	\n	\n
 	11:30-12:30 Lunch\n	\n	\n	12:30–14:00  Participant flash talks on thei
 r research and/or interests\n	\n\n\nDay 2\, Tuesday 2.2\n\n\n	\n	 9:00–
 11:30  HPC workflows with GROMACS supported by BioBB - bioexcel building 
 blocks / pycomms (Adam Hospital)\n	\n	\n	11:30-12:30 Lunch\n	\n	\n	12:30
 –14:00  GROMACS - Python down to the metal interface for in-memory tool
 chains with GROMACS (Eric Irrgang)\n	\n\n\nDay 3\, Wednesday 3.2\n\n\n	\n	
 9:00–10:30  pmx - free energy calculations or other of the above (Vytau
 tas Gapsys)\n	\n	\n	11:30-12:30 Lunch\n	\n	\n	12:30–14:00 Performant se
 tup  GROMACS on GPUs (Christian Blau)\n	\n\n\nLecturers: \n\n\n	Dr. Chri
 stian Blau\, Theoretical and Computational Biophysics\, KTH Royal Institut
 e of Technology\n	Dr. Yuriy Khalak\, Computational biomolecular dynamics g
 roup at the Max Planck Institute for Biophysical Chemistry\, Göttingen\n	
 Dr. Vytautas Gapsys\, Computational biomolecular dynamics group at the Max
  Planck Institute for Biophysical Chemistry\, Göttingen\n	Dr. Adam Hospit
 al\, Molecular Modelling and Bioinformatics\, Institute of Research in Bio
 medicine\, Barcelona\n	Dr. Eric Irrgang\, Department of Molecular Physiolo
 gy and Biological Physics\, University of Virginia\, Charlottesville\n	Dr.
  Dmitry Morozov\, Department of Chemistry\, University of Jyväskylä\n\n\
 nLanguage:   English\nPrice:           Free of charge (3 times
  2/3 training days)\n\nMaterials: The detailed agenda\, links to slides an
 d exercises and all questions asked and answered during the workshop can b
 e found at: \n\nhttps://a3s.fi/advanced_gmx/PRACE_CSC_BioExcelWorkshop-GRO
 MACS_workflows_and_advanced_topics.html\n\nREGISTRATION is OBLIGATORY sinc
 e the details to access the online course will be provided to the register
 ed and accepted attendees only. Participants will be selected based on ski
 lls\, motivation and maximum coverage of research groups. If you have regi
 stered to this course and you are not able to attend\, please CANCEL your 
 registration in advance by sending an email to patc@csc.fi\n\n \nhttps://
 events.prace-ri.eu/event/1148/
SUMMARY:[ONLINE] Advanced GROMACS workshop @ CSC
URL;VALUE=URI:https://events.prace-ri.eu/event/1148/
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