Organisers - John Harding (Sheffield University, United Kingdom)
- John Purton (Daresbury Laboratory, United Kingdom)
- Mario G. Del Popolo (Queen's University Belfast, United Kingdom)
Supports CECAM
 UK CCPs
DescriptionThe Basic Course
The first six days of the course will cover the basics of molecular simulation methods. Course notes will be provided. In addition to the course lectures, practical sessions will take place in which students will undertake relevant computational exercises. Further details and course timetable can be found on the CCP5 web pages http://www.ccp5.ac.uk/SSCCP5/main.html .
NB registration must be via the CCP5 web pages and not CECAM.
The lecture topics are as follows:
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- An Overview of Molecular Simulation (1 lecture, P.M. Rodger)
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- Statistical Mechanics (2 lectures, M. del Popolo)
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- Basic Molecular Dynamics (2 lectures, D. Willock)
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- Advanced Molecular Dynamics (2 lectures, D. Willock)
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- Non-Equilibrium Molecular Dynamics (1 lecture, P.M. Roger)
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- Monte Carlo Methods (4 lectures, P. Camp)
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- Free Energy Methods (2 lectures, P.M. Roger)
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- Long Ranged Forces (1 lecture, J.A. Purton)
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- Optimisation Methods (1 lecture, J. Harding)
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- Potentials (1 lecture, J.A. Purton)
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- Long timescale methods (1 lecture, J Harding)
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The Advanced Courses
Three advanced courses are given in the last three days of the course which run concurrently. The students choose one of these courses. Course notes are provided and there are accompanying computational lectures
First principles simulation (4 lectures given by Keith Refson; Rutherford-Appleton Lab)
Topics covered include
- Density-functional theory and the local-density approximation
- Aspects of the plane-wave pseudopotential (Car-Parrinello) implementation
- Some tricks of the trade and "folklore"
- Which properties can be calculated and how
- A case study of chemical changes
Mesoscale Methods ( 4 lectures given by Ian Halliday, Sheffield Hallam University)
Topics covered include
- Background. Why are mesoscale methods necessary and what are the areas of application?
- Mesoscale simulation strategies
- Lagrangian Hydrodynamics
- Lattice Gas Cellular Automata
- Lattice Boltzmann Methods
- Dissipative Particle Dynamics
Simulation of organic and biomolecules (4 lectures given by Xavier Daura, Autonomous University of Barcelona)
Topics covered include
- Biomolecular force fields: AMBER, CHARMM, OPLS, GROMOS; derivation of force field parameters; soft-core potentials.
- Assessing equilibration; energy analysis; structural analysis; principle-component analysis; calculation of entropy
- Replica-exchange molecular dynamics; weighted-histogram analysis
- Computation of NMR observables; calculation of spectra from simulation
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