Workshop on Gromacs & Advanced Simulation Methods

Clark Center @ Stanford University. April 7-8, 2008.

Background

We are happy to announce a special Gromacs workshop together with Michael Levitt & Vijay Pande at Stanford University. The scope of this workshop is to gather people working on new or otherwise advanced simulations algorithms, either in- or outside Gromacs, but that we believe could be interesting to support in the future. In contrast to the previous tuturials given e.g. in Helsinki, we will assume that the participants here are fairly comfortable with Gromacs, or at least MD simulations in general. We are planning two full days with a mix of formal talks, birds-of-a-feather sessions, and question-and-answer sessions in smaller groups. Most of, if not all, the main Gromacs developers plan to be present.

Topics covered

There are a couple of interesting topics that we have already selected:

The new domain decomposition parallelization in Gromacs 4.0, with some tips & tricks to get the most out of your hardware.
Different methods to perform free energy calculations. Slow-growth, perturbations, Bennett Acceptance Ratio. Which protocol is most efficient, and what new things will be in Gromacs 4.0?
QM/MM. How do you mix Quantum Mechanics with Gromacs?
Virtual sites for hydrogen motion removal and long time-steps
Membrane protein simulations
Replica exchange, and extracting kinetic data from it
Local pressure extensions to Gromacs
Gromacs source code walk-through

However, these are just examples. We would be particularly interested in participants who would like to contribute a small talk (anywhere from 15 to 45 mins) on their favorite subject, or you if have special requests about topics you'd like to learn more about.

Location

The workshop will be given in the Clark Center "Bio-X" building at Stanford University, 318 Campus Drive, Stanford CA, 94305. For more information and directions, have a look at http://biox.stanford.edu/clark/directions.html .
We start in S362 Monday April 7 at 9:00 am, and finish on Tuesday April 8 at 5:00pm.

Travel & accomodation

The easiest way to reach Stanford is to fly to San Francisco (SFO), or possibly San Jose (SJC) if you are traveling domestic. From the airport you can either take a shared-ride "shuttle" or use cheaper/slower public transportation. If you are coming by car, be warned that Stanford is cronically short of parking space, and it is particularly hard to find parking close to the Clark Center.

We have reserved a number of rooms at the Stanford/SLAC guest house for the duration of the workshop, but the block reservation is only valid until March 6, so book before then! The guest house is a quite nice hotel with free internet access located at the Stanford Linear Accelerator Center, with free shuttles going down to campus, the Clark Center, and downtown Palo Alto where it connects to Caltrain public transportation. You will have to make a reservation yourself with a credit card, but quite the group code "GROMACS" to get a slightly better rate. The guesthouse rooms are $89 for singles, and $119 for doubles (that are very large & nice...). Please share rooms if you can/want, since we could only reserve a limited number of rooms. The guesthose is staffed 24/7 - see http://guesthouse.stanford.edu, or call them at (650) 926-2800. If you prefer to stay downtown in Palo Alto (next to Stanford), one nice option is the Cardinal Hotel (http://www.cardinalhotel.com), and there are a bunch of cheaper motels along El Camino Real. Still, the guesthouse is probably the best value for money...

Cost?

It's free! We have all our travel covered by a collaboration grant, and we should even be able to treat you to coffee. However, you will have to take care of your own travel, accomodation, and food ;-)

Registration Info

Typically we would simply say "first come, first served", but since we plan to give another similar even soon in Göttingen, we will give priority to participants from the Americas and those willing to give brief presentations (remember, we want this to be two-way communication!) as long as they register the first two days.
Thus, start by filling in the form below, and wait for a confirmation email from Erik. Note that we the first round of confirmations won't be sent until Wednesday February 20, so I can do random selection based on the priorities above, just in case there is a gold-rush of early birds.
After that it will be first-come, first-served, irrespectively of where you are from!

While registration isn't binding, we ask you to only register if you will take part in the entire workshop (you are welcome to drop by anyway :-), and please let us know as soon as possible if you change your mind and decide not to come, so somebody else can use your slot!

Registration Form

Unfortunately the workshop is already full, so registration has closed.

Once again, very welcome to the workshop, and hope to see you in California & Palo Alto in April!

/Erik Lindahl