BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260715T183119Z UID:e50ecbef-8293-4fd8-8b67-79ddb87ee1cb DTSTART:20210622T070000Z DTEND:20210623T153000Z DESCRIPTION:Introduction to Molecular Modeling and Molecular Dynamics in HP C\n\nPurpose of the course\n\nThe purpose of this course is to present to existing and potential users of Molecular Dynamics packages the method\, t he necessary steps for a successful simulation\, common practices\, common mistakes. The steps for a complete simulation workflow i.e. system setup up to final properties evaluation will be presented using popular software packages.\n\nOutcomes\n\nAfter the course the participants should be able to efficiently use their prefered MD application (i.e. NAMD\, GROMACS\, L AMMPS\, CP2K)\, for molecular modeling and molecular dynamics simulations\ ,  how to create configuration files based on their needs\, tuning the mo dels\, how to efficiently use the resources based on the simulation detail s\, avoid common mistakes.\n\nPrerequisites\n\nBackground in Physics/Chemi stry/Biology. Programming skills\, aware of Parallel environments. \n\nThe hands-on sessions\, will take place on an HPC-like environment in a Virtu alBox image. Participants will be guided step by step on how to install an d use the VirtualBox at the beginning of hands-on sessions. \n\nCourse lan guage is English.\n\nRegistration\n\nRegistrations will be evaluated on a first-come\, first-served basis. GRNET is responsible for the selection of the participants on the basis of the training requirements and the techni cal skills of the candidates. GRNET will also seek to guarantee the maxim um possible geographical coverage with the participation of candidates fro m many countries.\n\nVenue\n\nONLINE using zoom\n\nARIS - System Informati on\n\nARIS is the name of the Greek supercomputer\, deployed and operated by GRNET (Greek Research and Technology Network) in Athens. ARIS consists of 532 computational nodes seperated in four “islands” as listed here: \n\n\n \n 426 thin nodes: Regular compute nodes without accelerator.\n \n \n 44 gpu nodes: “2 x NVIDIA Tesla k40m” accelerated nodes.\n \n \n 18 phi nodes: “2 x INTEL Xeon Phi 7120p” accelerated nodes.\n \n \n 44 f at nodes: Fat compute nodes have larger number of cores and memory per cor e than a thin node.\n \n \n 1 ml node : 8 x NVIDIA Volta V100 GPU accelera tors\n \n\n\nAll the nodes are connected via Infiniband network and share 2PB GPFS storage.The infrastructure also has an IBM TS3500 library of maxi mum storage capacity of about 6 PB. Access to the system is provided by tw o login nodes. \n\nAbout Tutors\n\nDr. Zoe Cournia (female) is a Researche r – Associate Professor level at the Biomedical Research Foundation\, Ac ademy of Athens\, where she works on anticancer drug design\, design of dr ug delivery systems and biomolecular modeling using computational techniqu es. She graduated from the Chemistry Department\, University of Athens in 2001 and completed her PhD at the University of Heidelberg in Germany in 2 006. She then worked as a postdoctoral researcher at the Chemistry Departm ent\, Yale University\, USA\, on computer-aided drug design and in 2009 sh e became a lecturer at Yale College. She has been awarded the American Ass ociation for Cancer Research Angiogenesis Fellowship (2008)\, the "Woman o f Innovation 2009" Award from the Connecticut Technology Council\, USA\, t he Marie Curie Fellowship from the European Union (2010)\, the "Outstandin g Junior Faculty Award" from the American Chemical Society (2014) and the first "Ada Lovelace Award" from the "Partnership for Advanced Computing in Europe" (2016). She is currently teaching at the Master’s program “In formation Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications\, National University of  Athens.\n\nD r. Dimitris Tsalikis (male) is a Research Associate at the Department of C hemical Engineering in the University of Patras. His research focuses on t he physicochemical characterization and the rheology of polymers\, polymer nanocomposites\, nanofluidics and formulations via atomistic and mesoscop ic simulations and to this he develops novel parallel computational method ologies. He received his Diploma in Chemical Engineering from the Universi ty of Patras in 2004 and his Ph.D. (titled: “Computational study of stru ctural relaxation and plastic deformation of glassy polymers”) from the National Technical University of Athens in 2009 under the advisement of Pr of. Doros N. Theodorou. In 2011 he joined the research team of Prof. Vlasi s Mavrantzas in Patras as a Research Associate. Dr. Tsalikis has a solid e xperience with high performance computing since 2007 being an active user of Tier1 and Tier0 HPC systems available to scientific community under the frameworks of HPC-Europa\, PRACE and LinkSCEEM projects. He is currently teaching at the Master’s program “Polymer Science and Technology” at University of Patras.\n\n Dr. Dellis (Male) holds a B.Sc. in Chemistry ( 1990) and PhD in Computational Chemistry (1995) from the National and Kapo distrian University of Athens\, Greece. He has extensive HPC and grid comp uting experience.  Currently he holds the position of “HPC Team leader ” at GRNET S.A.\n\nAbout GRNET\n\nGRNET - National Infrastructures for R esearch and Technology\, provides advanced network\, cloud computing and I T infrastructures and services to academic and research institutions\, to educational bodies at all levels\, as well as to agencies of the public\, broader public and private sector. It holds a key role as the coordinator of all e-infrastructures in education and research\, leveraging the educat ional and research activity in the country towards the development of appl ied and technological research. GRNET\, supervised by the Ministry of Digi tal Governance\, contributes to the country’s Digital Transformation via in-depth analysis\, technological studies\, standard solutions and specia lized know-how\, serving at the same time hundreds of thousands of users o n a daily basis in the strategic fields of Public Administration\, Educati on\, Research\, Health and Culture.\n\nMore at: https://grnet.gr/en/compan y/\n\nwww.grnet.gr\, hpc.grnet.gr\n\n \nhttps://events.prace-ri.eu/event/ 1228/ SUMMARY:[ONLINE] Introduction to Molecular Modeling and Molecular Dynamics in HPC @GRNET URL;VALUE=URI:https://events.prace-ri.eu/event/1228/ END:VEVENT END:VCALENDAR