AMBER Workshop 2014

 

Introduction

A number of workshops that teach Molecular Dynamics via practical introduction to the AMBER Molecular Dynamics Software have been taught over the years by Ross C. Walker and Adrian E. Roitberg assisted by other members of the AMBER development team.  

Recent workshops include:

  • Recife, Pernambuco, Brazil. 2013
  • Imperial College, London, UK. 2012
  • IRB-BSC, Barcelona, Spain. 2011
  • University of Dusseldorf, Germany. 2010
  • Sultan Qaboos University, Muscat, Oman, 2010
  • UC Merced, California, USA, 2009
  • University of Westminster, London, UK, 2009
  • Imperial College London, UK, 2008
  • University of Bergen, Norway, 2008

Sponsors

The workshop is supported by NVIDIA and the BSC Severo Ochoa Center of Excellence program. NVIDIA research explores challenging topics on the frontiers of visual, parallel, and mobile computing. NVIDIA supports advances in the field of physical simulation through collaboration with academic and industrial research institutions, and disseminate results in technical conferences, journals, and other academic venues.

NVIDIA will donate a Tesla K20C GPU that we will raffle among the attendees of the workshop.

Registration

The registration is now closed.

 

Registration fees are 190 euros.

Attendees are expected to bring their own laptop.

The organization will provide a pendrive with all necessary software and training material. Lunch and cofee breaks are included.

Organizing Committee

  • Ross C. Walker (University of California San Diego, USA) [Speaker]
  • Adrian E. Roitberg (University of Florida, USA)[Speaker]
  • Dwight McGee Jr. (University of Florida, USA)[Speaker]
  • Pablo D Dans (IRB Barcelona) [Speaker]
  • Federica Battistini (IRB Barcelona) [Speaker]
  • Modesto Orozco (Univ. Barcelona, INB, IRB, BSC, Spain)
  • Ramon Goñi (BSC, Spain)

Agenda

The duration of the meeting is 5 days, from 2nd of June to 6th. Typically there will be lectures 3 hours per day, and hands-on tutorials, about 5 hours per day. The content of the Workshop will include:

  • Molecular Dynamics with Amber
  • Using VMD to visualize AMBER
  • Dealing with non-standard residues
  • Building protein-ligand complexes
  • Statistical Mechanics for Free Energy Calculations
  • MM/PBSA calculations
  • Calculating relative binding free energies for protein/carbohydrate complexes
  • Enhanced sampling techniques
  • Maximizing Performance (Parallel Execution and NVIDIA GPU Acceleration)
  • Umbrella sampling simulations
  • Analyzing Simulations
  • Introduction to QM/MM Calculations
  • Lipid Simulations with AMBER

The target audience is graduate students and postdocs as well as a few
faculty interested in learning about Molecular Dynamics techniques. The
course is designed to introduce Molecular Dynamics techniques from an
introductory perspective but will progress quickly. Some experience with
the Linux operating system is essential but experience with AMBER or other
molecular dynamics packages is not required.

Recommended Hotels

The following are NOT in the city center, but close to the venue.

Hotel BONANOVA PARK (next to the BSC)
Address: Capità Arenas, 51 08034 Barcelona
Telephone: +34 93 204 09 00
Fax: +34 93 204 50 14
e-mail:
comercialbonanovapark@husa.es
Web:
www.hotelbonanovapark.com

Hotel HUSA ARENAS
Address: Capità Arenas 20, Barcelona
Telephone: +34 93 280 03 03
Fax: +34 93 280 33 92
e-mail:
hotelarenas@husa.es
Web:
www.husa.es

Residencia UNIVERSITARIA TORRE GIRONA (next to the BSC-5 minutes walking)
Address: Psg. Dels Til.lers, 19 08034 Barcelona
Telephone: +34 93 390 43 00
Fax: +34 93 205 69 10
e-mail:
torregirona@resa.es

Contact

Ramon Goni: ramon.goni(at)bsc.es