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DTSTAMP:20260710T224447Z
UID:ffd58a85-3bc8-45d3-9d58-79a0a6e881be
DTSTART:20201013T123000Z
DTEND:20201020T150000Z
DESCRIPTION:This online course is a collaboration between ARCHER2 Training 
 and BioExcel.\n \n\n\n\nThis online course consists of interactive hands-
 on practical sessions presented remotely using Collaborate. Attendees will
  be given access to ARCHER to execute the practical.\n\nOutline\n\nCP2K is
  a quantum chemistry and solid state physics software package that can per
 form atomistic simulations of a wide variety of systems\, ranging from sol
 id state to biological systems. CP2K provides a general framework for runn
 ing density functional theory (DFT) simulations\, with extensions that ena
 ble users to run classical molecular dynamics (MD)\, mix MD and DFT to obt
 ain quantum-mechanical/molecular-dynamics (QM/MM) runs\, or perform other 
 forms of metadynamics\, Monte Carlo\, or other simulations.\n\nThis course
  is aiming to teach attendees how to prepare and run biochemical simulatio
 ns in CP2K. Specifically\, we will be looking at how CP2K can be used to t
 rack the reaction dynamics of a system undergoing biological catalysis. In
  this course\, we shall be focusing on a Diels Alder transition taking pla
 ce in an immunoglobulin. We will begin by considering the reaction site in
  a purely quantum-mechanical method. Then\, we will slowly increase the co
 mplexity of the system to take into account the entire structure of the im
 munoglobulin (using QM/MM approach)\, the solution\, and finally\, we will
  add a ligand to the reaction.\n\nWhile we will be referencing some DFT an
 d QM/MM theory (mainly the nudged elastic band method and metadynamics)\, 
 this is not the principal aim of this course. Our aim is to use these syst
 ems to help familiarise attendees with using CP2K to run simulations of bi
 ochemical systems. CP2K can be used for non-biological systems\, and the t
 opics being taught here can be ported to other fields\, but this will not 
 be a primary focus of this course.\n\nLearning outcomes\n\nAt the end of t
 his session\, you will be able to:\n\n\n	 Run a geometry optimisation usi
 ng CP2K\n	 Run a frequency calculation using CP2K\n	 Estimate the energy
  barrier of a chemical reaction\n	 Run a nudged elastic band (NEB) simula
 tion to fine-tune the energy barrier and profile of a chemical reaction\n	
  Prepare a QM/MM simulation for CP2K\n	 Run a QM/MM simulation in CP2K\n
 \n\nPrerequisites\n\nWe ask that course attendees have the following:\n\n\
 n	 Familiar with basic bash functionality\n	 Know how to SSH\n	 Familia
 rity with a text editor (e.g. emacs/vim)\n	 Have attempted to login to AR
 CHER prior to the start of the course (credentials and instructions will b
 e supplied)\n\n\n \n\nOutline Timetable\n\nThe course will run over two T
 uesday afternoons\, 13th and 20th October.  Participants are expected to 
 attend both sessions\n\nEach session will run from 13:30-16:00  with a br
 eak 14:30-15:00.\n\nThere will be a follow-up consultancy session\, where 
 you can drop-in to ask questions of the tutor on Tuesday 3rd November 14:0
 0-16:00\n\n \nhttps://events.prace-ri.eu/event/1071/
SUMMARY:Practical introduction to QM/MM using CP2K for biomolecular modelli
 ng @ EPCC online
URL;VALUE=URI:https://events.prace-ri.eu/event/1071/
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