AMBER Archive (2006)

Subject: AMBER: AMBER Workshops, London UK 26th - 30th June 2006

From: Ross Walker (
Date: Tue May 02 2006 - 10:45:33 CDT

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 (
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:

Queries about either workshop should be sent by email to

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
- 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:- |
| | PGP Key available on request |

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