Preliminary GROMACS Workshop Schedule


Friday, September 13th
8:30–9 a.m. Registration and refreshments
9–10 a.m. Workshop welcome
10 a.m.–Noon Parallel breakout tutorial sessions (see below for details)
Noon–2 p.m. Lunch
2–4 p.m. Parallel breakout sessions (see below for details)
4:15–6 p.m. Plenary session: Erik Lindahl and Angel Garcia
6–7:30 p.m. Dinner
7:30–11 p.m. Poster session (MR5-2005 and atrium) and developer "office hours"
Saturday, September 14th
9–9:30 a.m. Chris Neale: Identifying hidden free energy barriers
9:30–10 a.m. Christoph Junghans: Adaptive resolution simulations with GROMACS
10–10:30 a.m. Ignacia Echeverria: Insight into the molecular origins of the internal friction in unfolded proteins
10:30–11 a.m. Break
11–11:30 a.m. Justin Lemkul: Insights into protein complexation and drug discovery from steered molecular dynamics simulations
11:30–Noon Per Larsson: Lipid tail protrusion could explain fusogenic activity in influenza hemagglutinin
Noon–2 p.m. Lunch
2–3:15 p.m. The future of GROMACS
3:15–5 p.m. Final plenary talk (Cecilia Clemente) and conference wrapup
Sunday, September 15th
10–Noon Brainstorming for new functionality for GROMACS 5.0 and beyond
Noon–2 p.m. Lunch
2–6 p.m. Collaborative debugging and coding


All sessions are in the MR5 auditorium unless otherwise noted.

Breakout Tutorial Sessions
Concurrent breakout sessions will be conducted by GROMACS developers and advanced users from the U.S. and Europe. Currently planned sessions are listed below. Click here for materials and sample files for most of the tutorials posted on the GROMACS web site.

Session 1a: 10 a.m.-12 p.m. (Beginner/Intermediate) MR5-2005
Mark Abraham "What's in a log file?," topology preparation and basic performance tuning.
Justin Lemkul Membrane simulations
Session 1b: 10 a.m.-12 p.m. (Intermediate/Advanced) MR5-1005
Michael Shirts Free energy calculation capabilities in GROMACS (including expanded ensemble and Hamiltonian Replica exchange)
Peter Kasson How long do I need to run my simulations?: A guide to thinking about convergence and sampling
Session 2a: 2 p.m.-4 p.m. (Beginner/Intermediate) MR5-2005
Justin Lemkul Computing potentials of mean force
Michael Shirts An introduction to free energy calculations
Mark Abraham An introduction to replica exchange simulations (temperature and Hamiltonian)
Session 2b: 2 p.m.-4 p.m. (Intermedate/Advanced) MR5-1005
Erik Lindahl Parallelization schemes and GPU acceleration
Iman Pouya Large-scale automated ensemble simulation with GROMACS & Copernicus

All conference sessions will be held in MR5, the Biomedical Engineering building, in the auditorium, MR5-2005, and MR5-1005. Signs will be posted at MR5 to directing people to the auditorium for the opening meeting.

Transportation in Charlottesville

Parking: For parking on Saturday and Sunday, the McLeod Hall Parking Garage is free all day and is your best bet, and is in the next building over from MR5. There are a number of other parking lots on campus open that day. For Friday, the proper location is the 11th St. Garage, on floor D or above. The 11th St. Garage is a couple of blocks from MR5, so plan 5 min or so to walk. Parking validation on Friday for the 11th St. Garage will be provided; we will distribute validation cards at the conference on Friday. Please notify the organizers beforehand so we have enough.

U.Va. Shuttles: The U. Va. shuttle system provides free shuttle service around campus, particularly from the Inn at Darden, where a number of people are staying. The conference building is at stop 55, on the corner of Lane and Jefferson Park Avenue. To travel from the Inn at Darden to MR5, the fastest option is likely as follows: take the Northline Connector to U-hall (Stop 91), and then take the Green Route to stop 55, which is right outside of MR5. Plan about 30 min for the trip. The website above has real-time schedule information.

Buses in Charlottesville: The Charlottesville Area Transit system provides bus service throughout Charlottesville. Fares are $0.75. If you are coming from a hotel just north of Charlottesville along Emmett St., then Route 7 will be your best bet. Stop 17028 (Jefferson Park Avenue (JPA) and Lane Road, near the covered walkway) is the closest to MR5; get off the bus, cross the street, backtrack half a block, and go down Lane Road. MR5 will be on your right. During the first session, we will poll to determine whether there are carpools we can organize to make travel easier.

Poster Session
The poster session will occur during a social hour that will also be used as "office hours" for GROMACS developers. Additionally, NVIDIA has donated two K20 compute GPUs as prizes encouraging participation at the poster session. Posters will be judged by steering committee members as well as additional judges from senior researchers attending the conference.

Plenary Sessions
A highlight of the conference will be a plenary presentation by Erik Lindahl and other developers on exciting future plans for GROMACS. In addition, three other well-known researchers with strong ties to the GROMACS community, Cecilia Clemente (Rice University), Angel Garcia (RPI), and Erik Lindahl (KTH Royal Institute of Technology), will disucuss their recent research.

Contributed Talks
These are designed to be research vignettes, with a theme of "How did I do [fill in cool application] with GROMACS?" GROMACS researchers, either developers or experienced "power users," will describe a particularly interesting discovery or powerful methodological advance, and include information on the approaches they used in order to achieve the results.

Informal interaction is one of the most important parts of scientific conferences. We have therefore scheduled long lunch and dinner breaks in order to increase this informal interaction. We are organizing "lunch with developers" so that junior attendees can have the opportunity for extended, small group interaction with developers as well as other senior participants.

Development Sessions
The last day, devoted to future development of GROMACS, is designed to be open to any attendee that wishes to participate in development plans, rather than being a closed day for current developers only. Conference attendees will thus be able to help shape the future development of the GROMACS code base.