BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260708T154754Z UID:11fc2346-3701-44f8-8505-91d17f10e043 DTSTART:20210422T073000Z DTEND:20210423T130000Z DESCRIPTION:\n\n\n\nDmitry Morozov (Chemistry\, University of Jyväskylä)\ ,\nEmiliano Ippoliti (Computational Biomedicine\, Forschungszentrum Jülic h)\,\nHolly Judge (EPCC\, University of Edinburgh)\n\n22 - 23 April 2021 9 :30-15:00 CEST (8:30-14:00 BST)\n\nOnline\n\n\n\n\n\n\nThis course is orga nised and funded by BioExcel - the Centre of Excellence for Computational Biomolecular Research (http://bioexcel.eu) and PRACE\, and delivered in co llaboration with ARCHER2 - the UK national supercomputing service (https:/ /www.archer2.ac.uk/).\n\n\n\n \n\n \n\n \n\nLearning outcomes\n\n\nThis course will equip participants to perform hybrid QM/MM simulations using the molecular dynamics code GROMACS in combination with the quantum chemis try package CP2K through an interface developed by one of the instructors from the BioExcel Centre of Excellence (www.bioexcel.eu).\n\nPrerequisites \n\n\nParticipants should be familiar with using GROMACS to perform molecu lar dynamics simulations. A background in computational quantum chemistry is not strictly required since an introduction of key aspects will be prov ided\, but previous familiarity is beneficial. You should be familiar with connecting to a remote machine using ssh and will benefit from experience using an HPC facility as you will execute hands-on practicals on the UK s upercomputer ARCHER2.\n\nDescription\n\n\nMost classical molecular mechani cs (MM) force fields are not sufficiently flexible to model processes in w hich chemical bonds are broken or formed. Instead\, some level of quantum mechanical (QM) description is needed to gain detailed mechanistic insight s into reaction mechanisms\, e.g. the catalytic action of enzymes\, and to compute photochemical properties such as absorption and emission spectra of fluorescent proteins. However biochemical systems (including solvent) a re too large to be solved in their entirety at ab initio QM level or effic iently even with a high-quality density functional theory (DFT) approximat ion. To overcome the cost of a QM description on the one hand versus the l imitations of a MM treatment on the other hand\, methods have been develop ed that treat a small critical region of interest at QM level while retain ing the computationally cheaper MM force field for the majority of the sys tem.\n\nDespite the simplicity of the QM/MM concept\, its application is c urrently restricted to a relatively small group of specialised expert user s often using in-house codes. To unlock the power of QM/MM simulations for the wider biomolecular simulation community\, the BioExcel Centre of Exce llence has developed an interface between the molecular dynamics code GROM ACS\, which is widely used in the biomolecular simulation community\, and the quantum chemistry package CP2K\, which supports calculations under per iodic boundary conditions with DFT methods.\n\nThis course explains key as pects relating to the use of QM/MM for biomolecular simulation with these two codes and equips participants with the ability to start using GROMACS and CP2K for this purpose in their own research. Participants are provided with the opportunity to gain hands-on practical experience running severa l example calculations on ARCHER2\, the UK national supercomputing service .\n\nTopics that will be covered are:\n\n\n Introduction to QM/MM a brief overview of:\n \n Relevant computational quantum chemistry\n QM-MM coupl ing\n Functionals\, basis sets\, pseudopotentials\, and dispersion\n \n \ n How to use GROMACS+CP2K to perform biomolecular QM/MM simulations\, incl uding:\n \n Umbrella sampling\n Energy minimisation\n Large phytochrome protein system setup\n Calculation of photochemical properties\n \n \n C P2K parameter choice guidance\, including:\n \n Checking convergence\n M odifying functional and basis set\n Performance\n \n \n\n\nSchedule\n\n\n (all times CEST)\n\nDay 1\n\n\n 9:30 Welcome\n 9:45 Lecture: Introduction to QM/MM I: computational quantum chemistry\n 10:15 Q&\;A\n 10:30 Break \n 10:45 GROMACS+CP2K Practical 1\n 12:00 Lunch\n 13:00 Lecture: Introduct ion to QM/MM II: QM-MM coupling\n 13:30 Q&\;A\n 13:45 Break\n 14:00 GRO MACS+CP2K Practical 2\n 15:00 Wrap up\n\n\nDay 2\n\n\n 9:30 Lecture: Intro duction to QM/MM III: functionals\, pseudopotentials\, dispersion correcti ons\n 10:00 Q&\;A\n 10:15 Break\n 10:30 Lecture &\; practical: CP2K parameter choice guidance\n 12:00 Lunch\n 13:00 GROMACS+CP2K Practical 3\n 14:30 Q&\;A\n 15:00 Wrap up\n\n\nRequirements:\n\nParticipants must br ing a laptop with a Mac\, Linux\, or Windows operating system (not a table t\, Chromebook\, etc.) that they have administrative privileges on.\n\nThe y are also required to abide by the ARCHER2 Training Code of Conduct.\n\nR egistration\n\n\nWe expect high demand for this course and places are limi ted to 30\, so we urge potential participants to register only if they mee t the prerequisites and expect to be able to take part. Recordings will be made available after the course on the BioExcel YouTube channel (https:// www.youtube.com/c/bioexcelcoe). Training materials such as practicals/tuto rials will appear on the BioExcel Github (https://github.com/bioexcel)\, h owever these will require installation of a custom version of GROMACS (htt ps://gitlab.com/aracsmd/gromacs/-/tree/2021.1-plumed-qmmm) that links with CP2K (this will be provided on ARCHER2).\n\nhttps://events.prace-ri.eu/ev ent/1204/ SUMMARY:QM/MM simulation with GROMACS + CP2K @ EPCC Online URL;VALUE=URI:https://events.prace-ri.eu/event/1204/ END:VEVENT END:VCALENDAR