[ONLINE] Introduction to Molecular Modeling and Molecular Dynamics in HPC @GRNET

ONLINE using zoom

ONLINE using zoom


Introduction to Molecular Modeling and Molecular Dynamics in HPC

Purpose of the course

The purpose of this course is to present to existing and potential users of Molecular Dynamics packages the method, the 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.


After the course the participants should be able to efficiently use their prefered MD application (i.e. NAMD, GROMACS, LAMMPS, CP2K), for molecular modeling and molecular dynamics simulations,  how to create configuration files based on their needs, tuning the models, how to efficiently use the resources based on the simulation details, avoid common mistakes.


Background in Physics/Chemistry/Biology. Programming skills, aware of Parallel environments.

The hands-on sessions, will take place on an HPC-like environment in a VirtualBox image. Participants will be guided step by step on how to install and use the VirtualBox at the beginning of hands-on sessions.

Course language is English.


Registrations 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 technical skills of the candidates. GRNET will also seek to guarantee the maximum possible geographical coverage with the participation of candidates from many countries.


ONLINE using zoom

ARIS - System Information

ARIS 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:

  • 426 thin nodes: Regular compute nodes without accelerator.

  • 44 gpu nodes: “2 x NVIDIA Tesla k40m” accelerated nodes.

  • 18 phi nodes: “2 x INTEL Xeon Phi 7120p” accelerated nodes.

  • 44 fat nodes: Fat compute nodes have larger number of cores and memory per core than a thin node.

  • 1 ml node : 8 x NVIDIA Volta V100 GPU accelerators

All the nodes are connected via Infiniband network and share 2PB GPFS storage.The infrastructure also has an IBM TS3500 library of maximum storage capacity of about 6 PB. Access to the system is provided by two login nodes.

About Tutors

Dr. Zoe Cournia (female) is a Researcher – Associate Professor level at the 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 University of Heidelberg in Germany in 2006. She then worked as a postdoctoral researcher at the Chemistry Department, Yale University, USA, on computer-aided drug design and in 2009 she became a lecturer at Yale College. She has been awarded the American Association for Cancer Research Angiogenesis Fellowship (2008), the "Woman of Innovation 2009" Award from the Connecticut Technology Council, USA, the Marie Curie Fellowship from the European Union (2010), the "Outstanding 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 “Information Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications, National University of  Athens.

Dr. Dimitris Tsalikis (male) is a Research Associate at the Department of Chemical Engineering in the University of Patras. His research focuses on the physicochemical characterization and the rheology of polymers, polymer nanocomposites, nanofluidics and formulations via atomistic and mesoscopic simulations and to this he develops novel parallel computational methodologies. He received his Diploma in Chemical Engineering from the University of Patras in 2004 and his Ph.D. (titled: “Computational study of structural relaxation and plastic deformation of glassy polymers”) from the National Technical University of Athens in 2009 under the advisement of Prof. Doros N. Theodorou. In 2011 he joined the research team of Prof. Vlasis Mavrantzas in Patras as a Research Associate. Dr. Tsalikis has a solid experience 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.

 Dr. Dellis (Male) holds a B.Sc. in Chemistry (1990) and PhD in Computational Chemistry (1995) from the National and Kapodistrian University of Athens, Greece. He has extensive HPC and grid computing experience.  Currently he holds the position of “HPC Team leader” at GRNET S.A.


GRNET - National Infrastructures for Research and Technology, provides advanced network, cloud computing and IT 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 educational and research activity in the country towards the development of applied and technological research. GRNET, supervised by the Ministry of Digital Governance, contributes to the country’s Digital Transformation via in-depth analysis, technological studies, standard solutions and specialized know-how, serving at the same time hundreds of thousands of users on a daily basis in the strategic fields of Public Administration, Education, Research, Health and Culture.

More at: https://grnet.gr/en/company/

www.grnet.gr, hpc.grnet.gr


    • 10:00 10:30
      Opening - Connection 30m
      Speaker: Dimitris Dellis (GRNET)
    • 10:30 11:00
      Introduction to PRACE
      Convener: Dr Dimitris Dellis (GRNET)
    • 11:00 12:00
      Introduction to molecular simulation
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 12:00 13:00
      Coarse-grained and atomistic simulation strategies
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 13:00 14:00
      Setup of simulation
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 14:00 15:00
      Break 1h
    • 15:00 16:00
      Real world examples and post simulation analysis
      Conveners: Dr Dimitris Dellis (GRNET) , Dr Zoe Cournia (Academy of Athens)
    • 16:00 17:00
      Visualization: VMD, PyMol, maps, GNUplot, Grace
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 17:00 17:45
      Quantum Molecular Simulation, Consistency, evaluation of results and efficient use of resources
      Convener: Dr Dimitris Dellis (GRNET)
    • 17:45 18:00
  • Wednesday, 23 June
    • 10:30 12:00
      Hands on workshop on MD biomolecular simulations: Setup of an MD simulation
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 12:00 12:15
      Coffe Break 15m
    • 12:15 14:00
      Hands on workshop on MD biomolecular simulations: Running and analyzing an MD simulation
      Conveners: Dr Dimitris Tsalikis (University of Patras) , Dr Zoe Cournia (Academy of Athens)
    • 14:00 15:00
      Lunch Break 1h
    • 15:00 17:00
      Hands on workshop on MD biomolecular simulations: Hands on workshop on MD biomolecular simulations (Running and analyzing an MD simulation)
    • 17:00 18:00