BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260711T122353Z UID:95c7ef9e-8e99-461e-8eb8-40454993782c DTSTART:20180423T070000Z DTEND:20180423T153000Z DESCRIPTION:Introduction to Biomolecular modelling and Molecular dynamics i n HPC\n\n(Classical and Quantum)\n\n23 April 2018\n\nPurpose of the course \n\nThe purpose of this course is to present to existing and potential use rs of Molecular Dynamics packages the method\, the necessary steps for a s uccessful simulation\, common practices\, common mistakes. The steps for a complete simulation workflow i.e. system setup up to final properties eva luation will be presented using popular software packages.\n\nOutcomes\n\n After the course the participants should be able to efficiently use their prefered MD application (i.e. NAMD\, GROMACS\, LAMMPS\, CP2K)\, for molecu lar modelling and molecular dynamics simulations\,  how to create configu ration files based on their needs\, tuning the models\, how to efficiently use the resources based on the simulation details\, avoid common mistakes .\n\nPrerequisites\n\nBackground in Physics/Chemistry/Biology. Programming skills\, aware of Parallel environments. Bring your own laptop in order t o be able to participate in the training hands on. Hands on work will be d one in pairs so if you don’t have a laptop you might work with a colleag ue. Course language is English.\n\nRegistration\n\nRegistrations will be e valuated on a first-come\, first-served basis. GRNET is responsible for th e selection of the participants on the basis of the training requirements and the technical skills of the candidates. GRNET will also seek to guara ntee the maximum possible geographical coverage with the participation of candidates from many countries.\n\nVenue\n\nGRNET headquarters\n\nAddress: 2nd  Floor\, 7\, Kifisias Av. GR 115 23 Athens\n\nInformation on how to reach GRNET headquarters ia available on GRNET website: https://grnet.gr/e n/contact-us/  \n\nAccommodation options near GRNET can be found at: htt ps://grnet.gr/wp-content/uploads/sites/13/2015/11/Hotels-near-GRNET-en.pdf \n\nARIS - System Information\n\nARIS is the name of the Greek supercomput er\, 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 426 thin nodes: Regular compute nodes without accelerator.\n \n \n 44 gpu nodes: “2 x NVIDIA Tesla k40m” acc elerated nodes.\n \n \n 18 phi nodes: “2 x INTEL Xeon Phi 7120p” accel erated nodes.\n \n \n 44 fat nodes: Fat compute nodes have larger number o f cores and memory per core than a thin node.\n \nAll the nodes are connec ted via Infiniband network and share 2PB GPFS storage.The infrastructure a lso has an IBM TS3500 library of maximum storage capacity of about 6 PB. A ccess to the system is provided by two login nodes. \n\nAbout Tutors\n\nDr . Zoe Cournia (female) is a Researcher – Assistant Professor level at th e Biomedical Research Foundation\, Academy of Athens\, where she works on anticancer drug design\, design of drug delivery systems and biomolecular modeling using computational techniques. She graduated from the Chemistry Department\, University of Athens in 2001 and completed her PhD at the Uni versity of Heidelberg in Germany in 2006. She then worked as a postdoctora l researcher at the Chemistry Department\, Yale University\, USA\, on comp uter-aided drug design and in 2009 she became a lecturer at Yale College. She has been awarded the American Association for Cancer Research Angiogen esis Fellowship (2008)\, the "Woman of Innovation 2009" Award from the Con necticut Technology Council\, USA\, the Marie Curie Fellowship from the Eu ropean Union (2010)\, the "Outstanding Junior Faculty Award" from the Amer ican Chemical Society (2014) and the first "Ada Lovelace Award" from the " Partnership for Advanced Computing in Europe" (2016). She is currently tea ching at the Master’s program “Information Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications\, National University of  Athens.\n\nDr. Dimitris Tsalikis (male) is a Rese arch Associate at the Department of Chemical Engineering in the University of Patras. His research focuses on the physicochemical characterization a nd the rheology of polymers\, polymer nanocomposites\, nanofluidics and fo rmulations via atomistic and mesoscopic simulations and to this he develop s novel parallel computational methodologies. He received his Diploma in C hemical Engineering from the University of Patras in 2004 and his Ph.D. (t itled: “Computational study of structural relaxation and plastic deforma tion of glassy polymers”) from the National Technical University of Athe ns in 2009 under the advisement of Prof. Doros N. Theodorou. In 2011 he jo ined the research team of Prof. Vlasis Mavrantzas in Patras as a Research Associate. Dr. Tsalikis has a solid experience with high performance compu ting since 2007 being an active user of Tier1 and Tier0 HPC systems availa ble 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. Del lis (Male) holds a B.Sc. in Chemistry (1990) and PhD in Computational Chem istry (1995) from the National and Kapodistrian University of Athens\, Gre ece. He has extensive HPC and grid computing experience. He was using HPC systems in computational chemistry research projects on fz-juelich machine s (2003-2005). He received an HPC-Europa grant on BSC (2009). In EGEE/EGI projects he acted as application support and VO software manager for SEE V O\, grid sites administrator (HG-02\, GR-06)\, NGI_GRNET support staff (20 08-2014). In PRACE 1IP/2IP/3IP/4IP/5IP he was involved in benchmarking tas ks either as group member or as BCO (2010-2017). Currently he holds the po sition of “Senior HPC Applications Support Engineer” at GRNET S.A. whe re he is responsible for activities related to user consultations\, portin g\, optimization and running HPC applications at national and internationa l resources.\n\nDr Aristeidis Sotiropoulos received his BSc in Computer Sc ience in 1998 from the University of Crete\, Greece and his PhD in Paralle l Processing and Cluster Computing in 2004 from the National Technical Uni versity of Athens\, Greece. His interests mainly focus on the fields of La rge Scale Computing &\; Storage Systems\, System Software for Scalable High Speed Interconnects for Computer Clusters and Advanced Microprocessor Architectures. He has published several scientific papers in internationa l journals and conference proceedings. He has received the IEEE IPDPS 2001 best paper award for the paper "Minimizing Completion Time for Loop Tilin g with Computation and Communication Overlapping". He has worked in severa l European and National R&\;D programs in the field of High Performance Computing\, Grid Computing\, Cloud Computing and Storage. In 2013\, he wa s appointed as the Head of Operations and Financial Management Services\, in charge of 15 people. Currently\, he is managing EC projects at GRNET SA \, the Greek NREN responsible for the provision of advanced e-infrastructu re services to the Greek Academic and Research Community.\n\nAbout GRNET\n \nGRNET provides Internet connectivity\, high-quality e-Infrastructures an d advanced services to the Greek Educational\, Academic and Research commu nity.\n\nThrough its high-speed\, high-capacity infrastructure that spans across the entire country\, GRNET interconnects more than 150 institutions \, including all universities and technological institutions\, as well as many research institutes and the public Greek School Network.\n\nGRNET ope rates the National High Performance Computing system (a Tier-1 in the Euro pean HPC ecosystem) and offers user and application support services\, tha t provide Greek scientists with the computing infrastructure and expertise they need for their research enabling them to perform large scale simulat ions.\n\nGRNET offers innovative IaaS cloud computing services to the Gree k and global research &\; education communities: “ ~okeanos” and “okeanos global” allow users to create multi-layer virtual infrastruct ure and instantiate virtual computing machines\, local networks to interco nnect them\, and a reliable storage space within seconds\, with few\, simp le mouse clicks.\n\nGRNET aims at contributing towards Greece’s Digital Convergence with the EU\, by supporting the development and encouraging th e use of e-Infrastructures and services. The right and timely planning str ategies\, together with the long experience and know-how of its people\, g uarantee the continuation and enhancement of GRNET’s successful course.\ n\nGreek Research and Technology Network – Networking Reserach and Educa tion:\n\nwww.grnet.gr\, hpc.grnet.gr\n\nhttps://events.prace-ri.eu/event/7 24/ SUMMARY:Introduction to Biomolecular modelling and Molecular dynamics in HP C @GRNET URL;VALUE=URI:https://events.prace-ri.eu/event/724/ END:VEVENT END:VCALENDAR