Free Energy Calculation and Molecular Kinetics Workshop

Event Date/s: From Tuesday 13 September 2016
To Thursday 15 September 2016

 

Organisers

Prof. Francesco Gervasio and Dr. Edina Rosta

 

network

Special invited lecturers

Academic:

Prof. John Chodera (Memorial Sloan-Kettering Cancer Center)
Prof. Nicolae-Viorel Buchete (University College Dublin)
Dr. Guillermo Pérez-Hernández, Dr. Jan-Hendrik Prinz (Free University Berlin)
Dr. Antonia Mey (University of Edinburgh)

Industry:

Dr. Mitsunori Kato (Novartis, Boston)
Dr. Ben Cossins (UCB Pharma, Slough)

 

Venue

Strand Campus, King’s College London, Strand, London WC2R 2LS. Room K4UI.12 and K4UI.13.

Directions to the room are available here:

http://www.modelsofauthority.ac.uk/blog/directions-to-k4u12/

 

Registration

Registration is free, but students will need to pay for their own travel and accommodation.

Please register via this link.

Accommodation

Students will need to organise their own accommodation. Short stay accommodation for King's College can be booked at

http://www.kcl.ac.uk/study/accommodation/other/visitors-accommodation or using local hostels.

Sponsors

CANES logoThe workshop is co-sponsored by the EPSRC Centre for Doctoral Training in Cross-Disciplinary Approaches to Non-Equilibrium Systems (CANES) programme, http://www.kcl.ac.uk/canes.

 

Overview

Free energies and kinetic properties are essential for the quantitative characterization of the physical properties of various systems modelled using molecular simulations. Often times, however, the time-scales of the important biomolecular processes are much longer than the simulation lengths that can be currently afforded with the high-performance supercomputing resources. Novel computational approaches are thus needed to bridge this gap using improved algorithms.


This workshop will provide a hands-on introduction to two of the most successful enhanced-sampling methods that are widely used to compute the free energy landscape and the kinetics associated with complex biomolecular events. In days 1 and 2, we will introduce the theory and practicalities of Markov models, showing how they can be used to calculate free energies and kinetics from biased and unbiased molecular dynamics trajectories. In day 3, we will introduce the theory of Metadynamics-based enhanced sampling approaches, followed by step-by-step tutorials for setting up and analyzing metadynamics simulations with the open-source plug-in PLUMED.
The workshop is aimed at advanced PhD students or post-docs who already have a working knowledge of molecular dynamics simulations of bio-molecular systems. During the 3 day training, the participants will become familiar with the free open-source program packages and learn to effectively use them in their own research. The workshop is open to advanced PhD students, postdoctoral fellows, and principal investigators, including participants from industry. Participants will be encouraged to share their experience with rare events in biomolecular systems and to try and apply the acquired knowledge on their own systems.


In addition to tutorials and workshop materials, we will also host talks from industry representatives, including molecular modelling experts from Novartis and UCB Pharma. 

Programme

Day 1. Introduction to Markov modeling analysis of molecular trajectories
(Edina Rosta, Vio Buchete, Adam Kells)

Link to program files: https://www.dropbox.com/sh/z2zmtzmkxrv2z2l/AAAW66zaF84NxW1GGJL-yV10a?dl=0
- Introduction to Markov models of biomolecular dynamics
- Simple practical introduction to reaction kinetics
- Free energies and dynamics from discretized reaction coordinate-based Markov models

13:00-13:15 Registration
13:15-14:00 Introduction to Markov models of biomolecular dynamics
14:00-14:20 Coffee break
14:20-15:00 Mitsunori Kato, Novartis

15:00-15:55 Hands-on tutorials
15:55-16:15 Coffee break
16:15-17:30 Hands-on tutorials

Day 2. Markov models from molecular trajectories
(Antonia Mey, Guillermo Pérez-Hernández, Jan-Hendrik Prinz, Frank Noe Group)
- Installation of the EMMA software (www.github.com/markovmodel/pyemma)
- Transformation and Clustering of biomolecular trajectory data
- Estimation and Analysis of MSMs
- Interpretation of the results

9:30-10:00 session 1 & setup
10:00-10:20 coffee break
10:20-11:20 session 2
11:20-12:00 Ben Cossins, UCB
12:00-13:50 lunch break 
13:50-14:20 John Chodera, Memorial Sloan-Kettering Cancer Center
14:20-14:50 session 3 
14:50-15:10 coffee break 
15:10-16:10 session 4 
16:10-16:30 coffee break 
16:30-17:30 session 5

Day 3. Metadynamics 
(Francesco Gervasio, Giorgio Saladino)

Link to program files: http://bit.do/KCL2016_plumed
- Introduction to Metadynamics and its main derivatives and variants.
- Introduction to Collective Variables (CVs) and their optimal choice.
- Combined approaches (parallel-tempering Metadynamics and Well Tempered Ensemble).
- Examples of PLUMED input used in recent papers (e.g. Sutto & Gervasio PNAS 2013).
- Setting up PLUMED calculations.
- Obtaining free energies from metadynamics simulations.
- Optimal and sub-optimal CVs.
- Convergence issues.
- Reweighting (obtaining the free energy as a function of different sets of CVs).

10:30-11:00 session 1
11:00-11:20 coffee break
11:20-12:20 session 2
12:20-13:50 lunch break 
13:50-14:50 session 3
14:50-15:10 coffee break
15:10-16:10 session 4
16:10-16:30 coffee break
16:30-17:30 session 5