PASI 2012 PROGRAM ~ SIRAH Forcefield

Workshop on Multiscale Modeling and Simulation

2012 NSF Pan American Advanced Studies Institute (PASI)

SUNDAY SEPTEMBER 2

Morning, Early afternoon – arrival

04:00 pm - 04:30 pm Workshop registration and check-in (conference hotel)

04:30 pm - 05:00 pm Opening Remarks (C. Abrams, S. Pantano, J. Pfaendtner)

05:00 pm - 07:00 pm Giovanni Bussi: Intro to MD and Thermostats

07:00 pm - 08:00 pm Get Together Party with refreshments @ Intercity Hotel

MONDAY SEPTEMBER 3

09:00 am - 10:00 am Giovanni Bussi: Crooks and Jarzynski/ Intro to rare events and CVs
10:00 am - 11:00 am Massimiliano Bonomi: Theory of simulated tempering and replica exchange

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Max Bonomi: Theory of umbrella sampling and SMD

12:30 pm - 02:00 pm Lunch

02:00 pm - 05:00 pm Hands-on workshop: PLUMED, monitoring CVs, PT, umbrella sampling and steered MD

TUESDAY SEPTEMBER 4 - - - WORKSHOP - - -

09:00 am - 09:30 am G. Bussi – research highlights
09:30 am - 10:00 amM. Bonomi – research highlights

10:00 am - 10:30 am S. Pantano – research highlights

10:30 am - 11:00 am Coffee Break

11:00 am - 12:00 pm J. Pfaendtner – research highlights
12:00 pm - 12:30 pm– B. Peters – research highlights

12:30 pm - 02:00 pm Lunch

02:00 pm - 03:00 pm Keynote Lecture 1: M. Parrinello

03:00 pm - 03:30 pm Coffee Break
03:30 pm - 04:00 pm C. Abrams – research highlights

04:00 pm - 04:30 pm M. Skaf – research highlights

WEDNESDAY SEPTEMBER 5

09:00 am - 10:00 am Leandro Martinez: Packmol

10:00 am - 11:00 am Baron Peters: Rare event and rate theory

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 am Keynote Lecture 2: Michele Parrinello

12:30 pm CULTURAL EXCURSION - Bouza Wine cellar

THURSDAY SEPTEMBER 6

09:00 am - 10:00 am Giovanni Bussi: Metadynamics from direct to well-tempered and flexible hills

10:00 am - 11:00 am Massimiliano Bonomi: Multiple walkers and combination of metadynamics with replica exchange methods

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 am Massimilano Bonomi: Path collective variables

12:30 pm - 02:00 pm Lunch

02:00 pm - 05:00 pm Hands-on workshop: Advanced PLUMED

FRIDAY SEPTEMBER 7

09:00 am - 11:00 am Baron Peters: Rare event and rate theory

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Leandro Martinez: Robust optimization strategies for the analysis of protein dynamics and model fitting

12:30 pm - 02:00 pm Lunch

02:00 pm – 05:00 pm Hands-on workshop: Baron Peters

SATURDAY SEPTEMBER 8

09:00 am - 10:00 am Leandro Martinez: The microscopic complexity of ligand binding dynamics and its implications to drug design

10:00 am - 11:00 am Sergio Pantano: SIRAH: a CG force field for biomolecular simulations

11:00 am - 11:30 am Coffee Break

11:30 am – 12:30 pm CFA: Getting and using your XSEDE account

12:30 pm - 02:30 pm BARBECUE AT IP MONTEVIDEO

02:30 pm – 04:30 pm Open discussion on Enhanced Sampling and Rates:

picking the right method for your problem

04:30 pm – 18:00 pm Coffee Break - Poster session and refreshments

MONDAY SEPTEMBER 10

09:00 am – 11:00 am SIRAH tutorial

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Monica Lamm: Force matching fundamentals

12:30 pm - 02:00 pm Lunch

02:00 pm - 05:00 pm Monica Lamm - Hands-on Workshop: Force matching

TUESDAY SEPTEMBER 11

09:00 am - 11:00 am Poster Session II

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Monica Lamm: Evaluating coarse-grain mapping schemes

12:30 pm - CULTURAL EXCURSION Walk around the old town and Lunch at

“MERCADO DEL PUERTO”

WEDNESDAY SEPTEMBER 12

09:00 am - 10:00 am Monica Lamm: Obtaining accurate dynamics from simulation with CG models

10:00 am - 11:00 am Roland Faller: Fundamentals of the Iterative Boltzmann Inversion (IBI)

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Faller/Lamm Research group highlights:

12:30 pm - 02:00 pm Lunch

02:00 pm - 03:00 pm Jim Pfaendtner/Alex Morriss-Andrews: Coarse-grained simulations of protein folding and aggregation
04:00 pm - 05:30 Hands-On Workshop on Coarse Grain

THURSDAY SEPTEMBER 13

09:00 am - 10:00 am Eric Vanden-Eijnden: Rare Events Theory

10:00 am - 11:00 am Roland Faller: Developing numerical potentials and their state point dependence

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Eric Vanden-Eijnden: Rare Events Numerical Implementation

12:30 pm - 02:00 pm Lunch

02:00 pm - 05:00 pm Hands-on workshop: EVE workshop

FRIDAY SEPTEMBER 14

09:00 am - 10:00 am Eric Vanden-Eijnden: Rare Events Applications

10:00 am - 11:00 am Roland Faller: Using the IBI for polymers

11:00 am - 11:30 am Coffee Break

11:30 am - 12:30 pm Eric Vanden-Eijnden:EVE