From owner-chemistry@ccl.net Tue May 2 14:27:00 2006 From: "Ross Walker ross.#%#.rosswalker.co.uk" To: CCL Subject: CCL: AMBER Workshops, London UK 26th - 30th June 2006 Message-Id: <-31659-060502114632-22154-JtA0oc4p6NXAzzogeimbEw#%#server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 2 May 2006 08:46:14 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross|*|rosswalker.co.uk] Eligibility Note: These workshops are currently open for registration by UK resident academics and students only. A more general registration will be held later if spaces are available. *********************************************************** The EPSRC National Service for Computational Chemistry Software is pleased to announce that it will be holding two workshops on the software package AMBER during the week of the 26th-30th June 2006. The first workshop (26th-27th June) will provide a basic introduction to the software package, while the second workshop (28th-30th June) will be an advanced course specifically geared around the new features in AMBER9. Both workshops will be held in the Chemistry Department at Imperial College London and will be given by Dr Ross Walker (The Scripps Research Institute & San Diego Supercomputer Center), Dr Mike Crowley (The Scripps Research Institute) and Dr Ian Gould (Imperial College London). Professor David Case (The Scripps Research Institute) will also be a tutor at the advanced workshop. AMBER is a software package for applying molecular mechanics, molecular dynamics and free energy calculations to simulate biomolecules. The workshops will consist of a series of short lectures followed by hands-on lab sessions that will cover use of the AMBER molecular dynamics software suite (http://amber.scripps.edu) and the theory behind it. There will also be opportunities for one-to- one discussions with the tutors for advice with specific research problems. Specific topics to be covered in each of the workshops are summarised below. Eligibility and Registration The workshops are open to all users and potential users of our service, and both academic staff and students in the UK are welcome. Registration is free but participants are expected to pay for their own travel and accommodation. Users may choose to register for one or both courses, but should be aware that the advanced course is really only suitable for people who have at least some background in molecular dynamics simulations. The deadline for all applications is Friday 9th June 2006. Application forms can be downloaded from the NSCCS website at: http://www.nsccs.ac.uk/amber_workshop2006.php Queries about either workshop should be sent by email to sarah.wilsey- -imperial.ac.uk. AMBER Basic Training Workshop: 26th - 27th June 2006 - An introduction to modelling and the principles of classical molecular dynamics including minimisation and dynamics algorithms, temperature regulation, pressure regulation and periodic boundary methods; implicit and explicit solvation models; the limitations of using a classical approach. - An introduction to each of the modules that make up the AMBER software suite, and a description of each of the different parameter sets available, the pros and cons of each and where to obtain help. - "Simple" peptide, protein and nucleic acid simulations including how to obtain a starting structure, creating prmtop and inpcrd files, running minimisations, gas phase and implicit solvent molecular dynamics, and how to view and analyse the results. - More advanced simulations of co-enzyme containing proteins and pharmaceutical compounds that require explicit parameters; how to create your own residues, including charge derivation and parameter selection. - An introduction to QM/MM coupled potential simulations. AMBER Advanced Training Workshop: 28th - 30th June 2006 - Solvation Energy Calculations with MMPBSA. - Advanced trajectory analysis (clustering, H-bond analysis, correlation functions...). - Reaction free energies with Thermodynamic Integration. - Reaction pathway sampling with QM/MM and nudged elastic band. - Replica Exchange MD. - Empirical Valence Bond Calculations. - Constant pH MD. - Considerations for setting up non-standard molecules. (Charge Derivation with R.E.D. and parameter selection). - Consideration for running simulations on parallel computers. Cluster design, bottlenecks, performance improvement, introduction to running simulations on supercomputers. - A selection of the most requested topics by applicants. *********************************************************** /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross- -rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.