Dates:   June 3 - 6, 2014

Venue: The meeting will be held in the new UCD O'Brien Science Centre - East, Room E1.17/1.18 (building 67 on UCD Map available here - Google Map - youtube video). Attention: on Friday, Day 4, New room H1.49 (nearby, towards the "Hub" building)

Getting to UCD, CECAM.IE & nearby hotels: http://www.ucd.ie/visitors

Interested participants should Apply directly by using the online form which is available in the CECAM Registered User Area: http://www.cecam.org/workshop-6-1043.html

New for 2014: There will be a poster session where all participants can present and discuss their recent research. Participants that intend to present a poster are encouraged to submit the poster title + authors list at the time of registration or via email.

Note: A limited number of rooms (single ensuite bedroom, free WiFi) in the UCD campus (UCD Glenomena Residence) is available for accepted participants at a rate of only €48 per night. Accepted participants can book their on-campus accommodation directly here and at: http://goo.gl/zKJAC2 .

Please note that the number of UCD on-campus rooms is small and that this housing option may not be available at all after May 12th, 2014.

For participants wishing to stay at a convenient nearby hotel, please note that the Stillorgan Park Hotel (http://www.stillorganpark.com) offers a special rate of €89 per night (including breakfast) to UCD visitors. Additional convenient housing is available at a variety of hotels in the larger Southern  Dublin area - please see: http://www.booking.com.

A list of airlines with direct flights to the Dublin Airport (DUB) is available here and here. Some online search engines for cheap flights to/from DUB are: Skyscanner, Kayak, or Orbitz. A convenient direct bus link to/from the airport (frequent, WiFi, online booking) is provided by Aircoach (online return ticket: ~€14, journey time ~40 mins). A taxi from the airport to the South Dublin/UCD area costs about €35.

Programme June 3-6, 2014:

Day 1

10:00 - Coffee, Registration, Posters Setup

11:00 to 11:45 Bernard Brooks, Vio Buchete and Lee Woodcock - Introduction

11:45 to 13:00   Bernard Brooks - CHARMM Basics

13:00 - Lunch Break

14:00 to 15.30  Alex MacKerell - The CHARMM Force Field

15:30 - Coffee Break

16:00 to 17:00 Antti-Pekka Hynninen - Optimizing CHARMM performance: a New Faster CHARMM Molecular Dynamics Engine

17:00 to 18:30 Poster Session I (posters to be displayed during days 1-2)

19:00 - Dinner

Day 2

9:30 to 11:00 Lennart Nilsson - CHARMM: Advanced Analysis

11:00 - Coffee Break

11:30 to 13:00 Wonpil Im - Membranes I: Protein Simulation: One Step Closer to Users

13:00  – Lunch Break

14:00 to 15:30 Richard Pastor - Membranes II:  Force Field, Correlation Functions, and Dynamics.

15:30 - Coffee Break

16:00 to 17:30 Richard Pastor -Membranes III: Mechanical Properties and Multicomponent Bilayers.

17:30 - Poster Session II (posters to be removed at the end of day 2)

Day 3

9:30 to 11:00 Lee Woodcock - Introduction to CHARMM, QM/MM

11:00 - Coffee Break

11:30 to 13:00 Edina Rosta - Enhanced Path Sampling with CHARMM-QChem

13:00 – Lunch

14:00 to 15:30 Victor Ovchinnikov - Conformational transitions and computing conformational free energy differences using CHARMM

15:30 - Coffee Break

16:00 to 17:30 Gerhard Koenig - Advanced Free Energy Methods

18:30 Dublin Literary Tour Pub Crawl

Day 4 - New Room H1.49 (near the old room, towards the "Hub")

10:00 to 11:00 Arjan van der Vaart  - Protein-DNA Simulations

11:00 - Coffee Break

11:30 to 13:00 Bernard Brooks - Replica Exchange & Enhanced Sampling Methods

13:00 - Lunch

14:00 to 15:30 Wei Yang - Random walk in orthogonal space to achieve efficient free energy simulation

15:30 to 16:00 Bernard Brooks - Poster Award and Closing Words

19:00 Dinner (speakers and organisers)

List of presenters (confirmed):

• Bernard Brooks (National Institute of Health (NIH, Bethesda, USA) – organizer
• Nicolae-Viorel Buchete (University College Dublin, Ireland) – organizer
• Antti-Pekka Hynninen (National Renewable Energy Laboratory, USA)
• Wonpil Im (Department of Molecular Sciences, University of Kansas, USA)
• Gerhard Koenig (NHLBI, NIH, USA)
• Alexander MacKerell (School of Pharmacy - University of Maryland, USA)
• Lennart Nilsson (Karolinska Institutet, Sweden)
• Victor Ovchinnikov (Harvard University, USA)
• Richard Pastor (LCB, NHLBI, National Institutes of Health, USA)
• Edina Rosta (King's College London, United Kingdom)
• Arjan van der Vaart (Univ. of South Florida, USA)
• Lee H. Woodcock (University of South Florida, Tampa, USA) – organizer
• Wei Yang (Florida State University, Tallahassee, USA)

DESCRIPTION:

The molecular simulation software CHARMM (Chemistry at HARvard Macromolecular Mechanics, see http://www.charmm.org) - used consistently in research studies for several decades - remains one of the most developed and used packages for the study of bio-molecular systems. Its important role in modern biomolecular simulations goes far beyond its extensive suite of codes and algorithms, however, it is mainly used by researchers in the US. The CHARMM Development Project involves a network of developers throughout the world working with Prof. Martin Karplus (Nobel Prize in Chemistry, 2013) and his group at Harvard to develop and maintain the CHARMM program.  CHARMM has evolved enormously since the early days, and has served as much as a development environment for the most advanced methods of molecular simulation, as well as a means of solving concrete problems with established theoretical and computational techniques. This meeting will address a strong interest of the research groups associated with CECAM within Ireland and with other CECAM nodes throughout the European Union. It will present an opportunity to discuss recent, advanced methods for molecular simulations and analysis that have been recently implemented in CHARMM. While recent years have seen a strong emergence in the research community of other molecular simulation programs, CHARMM retains a leading position through the number and quality of modern methods and algorithms that it incorporates. This meeting will focus on discussing in detail some of these more advanced methods. It will provide access to first-hand information and concrete examples on the modern simulation and analysis capabilities of the newest versions of CHARMM. A central theme of this meeting is that even new users of CHARMM should extract significant benefit from this experience for their own research. Advanced MD themes to be  discussed include  free energy calculations, multiscale simulations, enhanced sampling methods, and mixed quantum classical QM/MM calculations. This meeting, will create an opportunity for Irish and EU researchers to participate in oral presentations, discussions and poster presentations, together with some of the main CHARMM developers themselves. There will also be a focus  on the comparison of force field predictions and with experiments, as well as on enhanced sampling and kinetic analysis methods. There will also be an introduction to the latest developments in CHARMMing, an online facility that contains an integrated set of tools for uploading structures, performing simulations, and viewing and analysing the results.

The CCL Conference listing is available at: http://www.ccl.net/cca/info/conferencelist.shtml