[AMBER] AMBER Workshop Announcement - Haifa Israel, Sun Apr 26th to 30th.

From: Ross Walker <ross.rosswalker.co.uk>
Date: Tue, 27 Jan 2015 16:55:10 -0800

<<<please feel free to forward to anyone you feel may be interested in this workshop>>>

Dear All,

You are cordially invited to attend an AMBER Molecular Dynamics training workshop to be held at the Technion Institute in Haifa, Israel from Sun April 26th to Thur April 30th 2015. This workshop is being hosted jointly by the Bioinformatics Knowledge Unit of Technion, the AMBER Development Team and NVIDIA Inc.

Details and registration information can be found here:


Scope of the workshop:

This five day workshop will introduce researchers in the field of molecular simulations to the broad collection of computational toolsimplemented in the AMBER and AmberTools software packages for molecular dynamics (MD) simulations. It will consist of a combination of lectures and hands on tutorials that provide comprehensive introduction to molecular dynamics and molecular simulation focusing on practical application of version 14 of the AMBER MD software. The workshop consists of a series of short lectures followed by hands-on lab sessions that cover the use of AMBER and AmberTools and the theory behind it. There will be opportunities for discussion with thetutors for advice with specific research problems.

List of provisional topics:

        • Introduction to force fields and molecular dynamics.
        • Overview of AMBER and AmberTools and its programs.
        • Introduction to setting up and running simulations.
        • Visualizing AMBER simulations.
        • Overview of AMBER Force Fields / Solvent Models etc.
        • Introduction to implicit solvent and binding energy calculations.
        • Protein folding and advanced analysis.
        • Designing good simulation projects.
        • Dealing with non-standard residues.
        • What to do if there is no crystal structure.
        • Statistical mechanics for free energy calculations.
        • QM/MM coupled potential simulations.
        • Advanced sampling methods.
        • Lipid bilayer simulations.
        • GPU accelerated molecular dynamics simulations.

All students will receive a USB pen drive which contains all software and materials used in the workshop.

Workshop Instructors:

        • Professor Ross Walker (San Diego Supercomputer Center, UC San Diego, USA)
        • Professor Adrian Roitberg (Department of Chemistry, University of Florida, USA)
        • Professor Thomas Cheatham (Department of Pharmacology, University of Utah, USA)

Target audience:

Attendees are expected to be graduate students and postdocs as well as young lecturerswho have limited experience in molecular dynamics simulations and/or the AMBER and AmberTools software packages and would benefit from an introductory workshop that also covers advanced topics and the latestfeatures in the AMBER software, including GPU acceleration. The workshop will also be of use to those looking to convert from a different MD simulationpackage such as NAMD, CHARMM, Gromacs or Lammps.

Dates of workshop:

Sunday April 26th to Thursday April 30th 2015

Eligibility and Organization:

This workshop is open to everyone.

The event is organized by the Technion Institute, thus any questions may be directed to Dr. Fabian Glaser (fglaser.technion.ac.il) and not to the invited speakers/tutors.

Registration fee:

The registration fee, payable at the time of registering, is $200 USD and covers instructional materials including pen drives, refreshments and a workshop dinner. All participants are responsible for their own travel andaccommodation. Please contact Dr. Glaser for payment options.


Accommodation at the Technion is possible and will require additional payment. For housing information see: http://www.segeltechnion.org.il/TTFA/Templates/ShowPage.asp?DBID=1&LNGID=2&T%20MID=84&FID=572

Poster Session:

Although not mandatory participants are encouraged to bring posters highlighting their work for a poster session that will be held one evening during the workshop. A total of two NVIDIA K40 graphics cards will be given as prize to the best posters.

Application deadline:

Monday 30th March 2015*

*The number of places for this workshop is limited. If there is an unprecedented demand, we may have to restrict the number of people from the same research group. Please note that application may close early if all places have been filled before the deadline.

Application form:

Please visit the following web link for the online application form.


NVIDIA, Technion, The Moshe Yanai Fund for the Promotion of international Conferences

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Received on Tue Jan 27 2015 - 17:00:02 PST
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