**Due to the current uncertainty over the COVID situation the school will be taking place online.**

Organised by CCP5 and sponsored by CECAM, the School is intended for newcomers to the science of molecular simulation and will provide a comprehensive introduction to the theoretical background as well as practical sessions on computational methods and research seminars to illustrate the versatility of simulation in modern research. There will also be opportunities for participants to present their own research.

The Summer School starts with a two-day programming course, where students can opt to take either Python or modern Fortran. After this preparation, the first five days of the main School will cover the basics of molecular simulation, and the remaining three days will be devoted to more advanced courses with options in mesoscale, ab initio, and biomolecular simulation. Course notes will be provided in electronic format. In addition to the lectures, there will be extensive practical sessions in which students will undertake computational exercises to reinforce and further explore the material.

The school will take place between 11th and 22nd of July 2021 in online.

A fee of £50 to cover part of the expenses will be charged to successful applicants. The school has 50 to 100 places available. Successful applicants from last year’s delayed summer school will have an automatic reserve for this year’s online school and they will be receiving an email about this.

**Please note** The school can be recognized towards your doctoral training in UK, also upon request we can provide a letter for ECTS credits for your school.

Application deadline: 15th of April 2021 Acceptance decision: 1st of May 2021 Fee payments: 15th of May 2021

- Dr Colin Freeman, University of Sheffield
- Prof Neil Allan, University of Bristol
- Dr Mark Miller, University of Durham
- Dr Alin Elena, STFC Daresbury Laboratory

Please note the registration is handled externally by STFC For registration please click here

- Introduction to Modern Fortran (6 lectures, 4 practical sessions)
- Introduction to Python

- An Overview of Molecular Simulation
- Statistical Mechanics (2 lectures)
- Molecular Dynamics (3 lectures)
- Monte Carlo Methods (3 lectures)
- Free Energy Methods (3 lectures)
- Optimisation Methods
- Introduction to Force Fields
- Long timescale methods
- Advanced Free Energy methods
- Practicals (10 sessions over 5 afternoons)

- First principles simulation (6 lectures&hands-on tutorials)
- Mesoscale Methods (5 lectures)
- Simulation of Organic and Bio Molecules (6 lectures)
- Machine Learning for Interatomic Potentials (xxx)

- Prof Mike Allen (University of Bristol)
- Prof John Harding (University of Sheffield)
- Prof Neil Allan (University of Bristol)
- Prof Jamshed Anwar (University of Lancaster)
- Prof Paola Carbone (University of Manchester)
- Dr Livia Bartok-Pártay (University of Warwick)
- Dr Marcus Campbell Bannerman (University of Aberdeen)
- Dr Colin Freeman (University of Sheffield)
- Dr Alin Elena (Daresbury Laboratory)

- Prof Keith Refson (Royal Holloway, University of London)
- Prof Stewart Clark (University of Durham)
- Dr Barry Searle (Daresbury Laboratory)

- Dr Ian Halliday (Sheffield Hallam University)
- Dr Michael Seaton (Daresbury Laboratory)

- Prof Haider Shozeb (University College London)
- Prof Charles Laughton (University of Nottingham)
- Dr Sarah Fegan (Daresbury Laboratory)

- Prof Gábor Csányi (University of Cambridge)
- TBC
- TBC

- Dr Marcus Campbell Bannerman (University of Aberdeen)
- Dr Alin Elena (Daresbury Laboratory)

** Provisional and Subject to change**

Date | Activity | Location |
---|---|---|

July 12 |
||

9:00 - 10:00 | Fortran I/Python I AE/MB | |

10:00 - 11:00 | Fortran II/Python II AE/MB | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Fortran III/Python III AE/MB | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practicals | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:30 | Practicals | |

July 13 |
||

9:00 - 10:00 | Fortran IV/Python IV AE/MB | |

10:00 - 11:00 | Fortran V/Python V AE/MB | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Fortran VI/Python VI AE/MB | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practicals | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:30 | Practicals | |

July 14 |
||

9:00 - 10:00 | Overview of molecular simulations - PC | |

10:00 - 11:00 | Statistical Mechanics 1 - MB | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Statistical Mechanics 2 - MB | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practical - Stat Mech Problems | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals - Basics | |

17:10 - 18:10 | Invited Speaker 1 | |

July 15 |
||

9:00 - 10:00 | Introduction to force fields - PC | |

10:00 - 11:00 | Monte Carlo 1 - NA | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Monte Carlo 2 - NA | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practical - MC integration | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals - Intro to MC | |

17:10 - 18:10 | Invited Speaker 2 | |

July 16 |
||

9:00 - 10:00 | Molecular Dynamics 1 - CF | |

10:00 - 11:00 | Molecular Dynamics 2 - CF | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Monte Carlo 3 - MA | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practical - Intro to MD | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals - Phase Equilibria | |

17:10 - 18:10 | Invited Speaker 3 | |

July 17 |
||

9:00 - 10:00 | Molecular Dynamics 3 - MA | |

10:00 - 11:00 | Free energy methods 1 - JA | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Free energy methods 2 - JA | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practical - Thermostats+ shake | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals - Stability + accur MD | |

17:10 - 18:10 | Invited Speaker 4 | |

** July 18 Free day ** | ||

July 19 |
||

9:00 - 10:00 | Optimisation methods - JH | |

10:00 - 11:00 | Long timescale methods - JH | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Advanced Free Energy - LBP | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practical - Chemical potential | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals - Forcefields optimisation | |

17:10 - 18:10 | Research Seminar | |

19:00 - | School Dinner | |

July 20 |
||

9:00 - 10:00 | Advanced Seminar 1 | |

10:00 - 11:00 | Advanced Seminar 2 | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Advanced Seminar 3 | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practicals | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals | |

17:10 - 18:10 | Invited Speaker 5 | |

July 21 |
||

9:00 - 10:00 | Advanced Seminar 4 | |

10:00 - 11:00 | Advanced Seminar 5 | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Advanced Seminar 6 | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practicals | |

15:30 - 16:00 | Refreshments | |

16:00 - 17:00 | Practicals | |

July 22 |
||

9:00 - 10:00 | Advanced Seminar 7 | |

10:00 - 11:00 | Practicals | |

11:00 - 11:30 | Refreshments | |

11:30 - 12:30 | Practicals | |

12:30 - 14:00 | Lunch | |

14:00 - 15:30 | Practicals |

Advanced Seminars may be structured different depending on the lecturers.

We put together a fine list of speakers to inspire you in molecular simulations.

If you opted to give an oral presentation, we will make a selection of 4-5 talks.

Keep in mind for poster size is A0 maximum.

For more information do not hesitate to contact Alin M Elena alin-marin.elena@stfc.ac.uk

An overview of the current state of molecular simulation with examples of special interest taken from the literature.

In this lecture we will begin with an important question: why bother with statistical thermodynamics? We will progress to basic statistical quantities and concepts such as averages, fluctuations and correlations and how to use them in practice to calculate the physical properties of systems. This will lead us to the determination of the true statistical error for system properties obtained by simulation. We will apply these ideas to commonly calculated properties such as diffusion, radial distribution functions and velocity autocorrelation, while also examining the physical meaning of these properties. We will conclude with a look at distribution functions: how they arise and what they mean.

In the second lecture we shall look at more theoretical aspects of statistical mechanics. Beginning with the Lagrange and Hamiltonian description of classical mechanics we shall progress to the idea of phase space and the concept of a probability distribution function. This will be followed by basic applications (and associated mathematical manipulations) of the distribution function to obtain various physical properties of a system. We will examine the common ensembles (NVE, NVT and NPT) and discuss their application and interrelation. Finally we shall look at time dependence, beginning with the Liouville Equation and its connection with other time dependent equations. We shall conclude with the fluctuation-dissipation theorem.

Basics: The system. Random sampling. Importance sampling. Detailed balance. Metropolis algorithm in the canonical ensemble. Isothermal-isobaric ensemble. Grand-canonical ensemble. Which ensemble?

Practicalities: Finite-size effects. Random number generators. Tuning the acceptance rate. Equilibration. Configurational temperature. Ergodicity and free-energy barriers. Measuring ensemble averages. Examples (showing ensemble independence for the Lennard-Jones fluid)

(Free) Energy Barriers: Quasi non-ergodicity. Vapour-liquid phase transition as an example. Removing the interface by Gibbs ensemble MC. Free-energy barrier in the grand-canonical ensemble. Multicanonical preweighting. Histogram reweighting. Parallel tempering

Molecular dynamics: the basic methodology. Integration algorithms and their derivation. Static properties: thermodynamics and structure. Dynamic properties: correlation functions and collective properties

Practical aspects of molecular dynamics - Verlet neighbour list, link cell algorithm. Calculating pressure: the virial theorem and the thermodynamic method. Estimating statistical errors: the blocking method. Symplectic algorithms and the Tuckerman-Berne-Martyna approach.

Extended systems: canonical (NVT) and isothermal-isobaric (NPT) ensembles. Rigid Bodies, SHAKE, RATTLE.

Free energy, chemical potential & thermodynamics. Applications. Essential statistical mechanics. Ensemble averages, probability distributions & simulations. Free energy, the challenge. Particle insertion & removal. Energy density distributions. The perturbation method.

Review essential statistical mechanics. Thermodynamic integration. Potential of mean force calculations. Umbrella sampling. Absolute free energies. Free energy of liquids.Free energy of solids.

The energy landscape, geometrical optimisation and saddle points. Minimisation methods (steepest descent, conjugate gradient, genetic algorithm). Saddle-points (transition state theory, harmonic theory, nudged elastic band, dimer method).

Long timescales simulations - the problems. Transition state theory and kinetic Monte Carlo. Temperature accelerated hyperdynamics. Metadynamics.

TBD

First-principles simulation has grown to become one of the most influential and important techniques for modelling at the atomic level. With nuclei and electrons as the basic ingredients the system is modelled at a deeper level of physics than with atoms and interatomic potentials. By explicitly including the electrons in the model and treating their interactions using quantum-mechanical laws, chemical bonding arises as an emergent phenomenon of the model. All kinds of bonding - ionic, covalent, metallic, hydrogen can be treated using the same method. The price of this accurate Hamiltonian is a computational cost orders of magnitude higher than atomic potential models. Nevertheless it is possible and convenient with modern parallel computers to simulate systems of hundreds of atoms, and perform optimization and molecular dynamics in a variety of ensembles.

In this advanced course I will provide a rapid introduction to the “nuts and bolts” of first-principles simulation. In accordance with the philosophy of the CCP5 Summer School, the aim is to attempt to open up the “black box” and explain the concepts and algorithms used. The presentation will assume a familiarity with wave mechanics at the undergraduate level and Dirac notation.

In the practicals you will be able to try for yourself using an advanced density functional code. You should be capable of running realistic calculations by the end of the course, and aware of the major aspects of setup and testing that are vital ingredients for success. The practicals will consist of a series of guided exercises with the CASTEP and CRYSTAL codes.

- Motivation
- Quantum-Mechanical approaches
- Density-Functional Theory
- Excited states: TD-DFT
- Electronic Structure of Condensed Phases
- Total-energy calculations
- Basis sets
- Plane waves and pseudopotentials
- How to solve the equations
- Ab-initio simulations

- Convergence
- Structural Calculations
- Lattice Dynamics
- Exchange and Correlation Functionals
- Summary

The lecture notes from the CASTEP workshop held in 2007 are available from http://www.castep.org. Links to a number of ab-initio methods and resources are available at http://electronicstructure.org/.

Mesoscale methods of modelling are capable of tackling larger length and time scales than those available using atomistic methods. By using particles considerably larger than atoms and appropriate choices of interactions between them, these techniques can readily model bulk materials and large structures at the cost of omitting some fine atomic detail. Hydrodynamics start to become more important at these scales: these modelling techniques are thus designed to ensure correct (emergent) fluid behaviour. A mesoscale model can be set up either using a ‘bottom-up’ approach from atomistic models, a ‘top-down’ approach from continuum fluid models, or both.

In this advanced course we will provide an introduction to two mesoscale methods: Dissipative Particle Dynamics (DPD) and the Lattice Boltzmann Equation (LBE) method. We will explain the origins, concepts and algorithms of both methods, as well as their applications, continuing developments and how they can be related to material models at smaller and larger scales (including those covered by the basic lectures).

In the practicals, you will be able to try out DPD and LBE using both simple ‘hackable’ codes and the general-purpose mesoscale modelling package DL_MESO. By the end of the course, you will gain insight into the capabilities of both mesoscale modelling methods. The practicals will consist of a series of guided exercises using the provided codes.

- Techniques
- Physical scales
- Mesoscale simulation strategies

- DPD algorithm
- Fokker-Planck formulation
- Application to simple/complex fluids
- Boundary conditions
- Thermodynamics and DPD
- Molecular dynamics and DPD

- Classical Boltzmann/Boltzmann Bhatnagar-Gross-Krook (BGK) Equations
- Lattice Gas Cellular Automata (LGCA)
- Multiple component or “diphasic” LGCA
- Lattice Boltzmann Equation method
- Lattice Boltzmann BGK Equation and kinetic theory
- LBE for multi-component flow

Biomolecular systems can include proteins, DNA, lipids and the small molecules that interact with them. Individual residues, such as amino acids or nucleic acids, combine to form large complex macromolecules. Here we will focus on how simulation tools like those you have learned about in the summer school can be used to study the structure and function of biomolecules.

This advanced course will cover everything from setting up a biomolecular system for simulation to analysing the results. In addition to the standard molecular dynamics, enhanced sampling methods (including metadynamics), free energy methods and multiscale methods will be explained. One lecture will be devoted to nucleic acids. There will be hands-on practical sessions to accompany each of the lectures.

- Biomolecules
- Molecular Dynamics Software
- Force Fields for Biomolecules

- Errors/problems in PDB files
- Checking/choosing protonation states
- Solvation
- Analysis: assessing convergence and sampling

- Replica exchange methods
- Biased sampling: methods based on modified Hamiltonians
- Biased sampling: methods based on unmodified Hamiltonians

- DNA

- QM/MM
- Coarse-graining
- Code Coupling

- Ligand Binding
- FEP
- Alchemical Perturbations

to be added soon