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Introduction to event-driven molecular simulation using DynamO

Event Details

This workshop introduces the dynamics of particles that interact with discrete-potentials and how to perform simulations of these systems using the DynamO software package.  This relatively new, open-source code is targeted solely at discrete potential systems.

The simplest example of a discrete-potential system is the hard-sphere fluid; however, more complex systems can be developed by introducing additional "steps" in the potential, beginning with the square-well potential and more complicated multi-step potentials.  These models underpin a wide range of theoretical treatments, such as kinetic theory and thermodynamic perturbation theory, but they cannot be directly simulated using standard packages (e.g., DL_POLY).  The discontinuous changes in the interaction energy lead to impulsive forces that are incompatible with standard numerical integration techniques, and they must instead be treated using an event-driven approach.  This workshop will introduce the event-driven simulation methods, and outline key concepts through practical sessions carrying out simulations using the DynamO software package.

Topics:

  • Introduction to event-driven simulation and discrete potentials.
  • Installation and structure of the DynamO software.
  • Equilibrium simulation of simple discrete fluids using DynamO
    • Simulation of single and multi-component hard-sphere, square-well, and stepped Lennard-Jones fluids.
    • Determination of the radial distribution function, pressure, and transport properties (viscosity, thermal conductivity/diffusivity, self/mutual diffusion coefficient).
  • Non-equilibrium simulation of simple discrete fluids: Compression/packing, Lees-Edwards boundary conditions, Thermostats, and heated walls.
  • Polymeric fluids, linear/ring/star polymers.
  • Simple off-lattice models for protein folding: Square-well homopolymer, HP model

 

AGENDA 

NOTE: Each tutorial session will begin with a 15 minute introductory talk followed by a hands-on session.

09:30-10:00         Registration (coffee available)

10:00-11:00         Introductory talk: Event-driven simulation, discrete potentials, and DynamO.

11:00-12:00         Equilibrium simulation of simple discrete fluids. This session walks through the simulation of simple discrete fluids to calculate static properties, such as the equation of state and radial distribution function. This repeats the one of the key preliminary results of event-driven simulation, the discovery of an entropic freezing transition in hard-spheres.

12:00-13:00         Lunch (vouchers provided to be used in either Starbucks or the Lab Restaurant)

13:00-14:00         Transport properties of mixtures: In this session, mixtures of fluids and their equilibrium transport properties are introduced. Effects such as viscosity, thermal conductivity, and thermophoresis are explored along with their dependence on the model/molecular parameters. Non-equilibrium techniques are also introduced as a method for improving accuracy.               

14:00-15:00         Complex systems/Polymeric fluids:  This shorter session illustrates how to set up and pack a complex system interaction system within DynamO. This uses the simulation of a simple polymeric fluid as an example and applies techniques in the previous sessions to characterise this model system.

15:00-15:30         Coffee Break

15:30-16:30         Models for protein folding: This session introduces a simple model for protein folding. These systems are extremely difficult to equilibrate, and so they are used to illustrate the multi-canonical and parallel tempering facilities of DynamO. A revolutionary result on the why the helix structure is seen so often in nature (e.g., DNA) is repeated.

16:30-17:00         Questions / Discussion 

17:00                     Close

 

Organising Committee

Marcus Campbell Bannerman (University of Aberdeen)
John Purton (STFC Daresbury Laboratory)
Leo Lue (University of Strathclyde)



Start Date: Friday, 23rd January 2015
End Date: Friday, 23rd January 2015

Price: £0
Fee Info: Registration is FREE for this workshop. However, if you register for the event and then do not attend you will be charged a "no show" fee of £25. All cancellations MUST be received before 12pm on Friday 16th January 2015. Cancellations received after this will be charged a cancellation fee of £25.

Spaces Available

22 remaining out of 40 spaces

View list of delegates

Venue Details

Brunner-Mond Training Suite
A56, STFC Daresbury Laboratory
Venue Website

Accommodation Details

Accommodation is NOT included with your registration for this event. If you require accommodation a list of local hotels is available to download from the top of the page. Prices included are an indication only and should be checked before booking.
For further information contact Meeting Administrator