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Advances in Biomolecular Modelling and Simulations using CHARMM

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Dates:   June 3 – 6, 2014

Venue: The meeting will be held in the new UCD O’Brien Science Centre – East (building 67 on UCD Map available hereGoogle Mapyoutube video).

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 1: There is a 200 registration fee that covers the tutorial dinner, coffee breaks and other meeting expenses. PhD students and Postdoctoral Fellows can apply for a fee waiver if they will submit their CECAM application online before May 1st, 2014!

Note 2: 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 Proposed for 2014:

Day 1
10:00 to 11:00 – Registration and Coffee & Posters Setup
11:00 to 13:00 Bernard Brooks, Vio Buchete and Lee Woodcock – Introduction
13:00 to 14:00 – Lunch
14:00 – 15.15  Lennart Nilsson – CHARMM Basics
15:15 to 15:45 Introduction of Posters
15:45  to 16.15 Coffee Break
16:15 to 17:30 Arjan van der Vaart  – Free Energy Simulations (FES) (hands-on research examples)
17:30 to 19:00 Poster Session (posters to be displayed during days 1-3)
19:30 – Dinner 1

Day 2
09:30 to 11:00 Alex MacKerell – The CHARMM Force Field
11:00 to 11:30 – Coffee Break
11:30 to 13:00 Lennart Nilsson – CHARMM: Advanced Analysis (hands-on research problems)
13:00 to 14:00 – Lunch
14:00 to 15:15 Gerhard Koenig – Advanced Free Energy Methods (hands-on research problems)
15:15 to 16:15 – Poster Session & Coffee Break
16:15 to 17:30 Victor Ovchinnikov – Conformational transitions and computing conformational free energy differences using CHARMM

Day 3
09:30 to 11:00 Wonpil Im – Membrane Protein Simulation: One Step Closer to Users (hands-on research problems)
11:00 to 11:30 – Coffee Break
11:30 to 12:45 Richard Pastor – Simulations of Lipid Bilayers in CHARMM; Mechanical Properties of Peptide-Membrane Systems
13:00 to 14:15 – Lunch
14:15 to 15:15 Antti-Pekka Hynninen – Optimizing CHARMM performance: a New Faster CHARMM Molecular Dynamics Engine
15:15 to 16:00 Edina Rosta – Enhanced Path Sampling with CHARMM-QChem (hands-on research problems)
16:00 to 16:30 – Coffee Break
16:30 to 17:30 Lee Woodcock – Introduction to CHARMM-QChem (hands-on research problems)
19:30 to 21:30 – Dinner 2

Day 4
09:30 to 10:00 Lee Woodcock – More Information on Using CHARMM-QChem
10:00 to 11:00 Wei Yang – Random walk in orthogonal space to achieve efficient free energy simulation
11:00 to 11:30 – Coffee Break
11:30 to 13:00 Bernard Brooks – Novel Enhanced Sampling Methods
13:00 to 14:00 – Lunch
14:00 to 15:00 Vio Buchete – Kinetic Analysis of Replica Exchange Trajectories
15:00 to 16:00 Bernard Brooks – Poster Awards & Closing Word

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

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