CCP5 Summer School 2020

Molecular simulation methods


Due to COVID-19 the school is postponed to July 2021

About


COVID-19 Information

With regret, the organising committee and CCP5 have decided to postpone the Summer School until next year due to the coronavirus outbreak. We have decided against running the School remotely because we believe that it is important for the new generation of computational scientists to meet each other in person. Direct interactions, both socially and in the classes, are an essential part of the School’s purpose. We expect to announce firm dates for 2021 this summer.

We will soon send provisional offer letters to successful applicants. We realise that not everyone will want or be able to attend in 2021, so you are free to accept of reject the place. No payment will be due immediately, and arrangements for payments will be communicated closer to the dates in 2021 after confirmation of participation. Please inform us immediately if someone contacts you for any payment this year, since it is likely to be a scam. Applicants who are not accepted based on their application to the 2020 School may apply again for a place in 2021. We hope to expand the capacity of the School in 2021 to make up for the lost year.

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 addition to the lectures, there will be extensive practical sessions in which students will undertake computational exercises to reinforce and further explore the material.

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.

There are no funds available for travel support or waiving the fee.

Key dates

TBD

Organising Committee

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

Sponsors

Registration


Registration is closed now.

Lectures


Programming Courses

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

Basic Courses

  • 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)

Advanced Courses

Lecturers

First principles simulations

Mesoscale methods

Simulation of organic and biomolecules

Programming

Timetable


TBD

Research Seminar Speakers


Campus information


How to make it to Durham University

University instructions

Student Events


Student Seminar (13+2 minutes)

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

CCP5 Student Poster Prize

Keep in mind for poster size is A0 maximum.

CCP5 Student Talk Prize

Contact


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

Overview basic lectures


An Overview of Molecular Simulation

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

Introduction to force fields

Statistical Mechanics 1

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.

Statistical Mechanics 2

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.

Monte Carlo 1

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

Monte Carlo 2

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)

Monte Carlo 3

(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 1

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

Molecular dynamics 2

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.

Molecular dynamics 3

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

Free energy methods 1

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.

Free energy methods 2

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

Optimization Methods

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 timescale methods

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

Advanced Free Energy Methods

TBD

First-principles simulation


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.

Synopsis

An Introduction to First-Principles Simulation

  • 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

Practical calculations using first-principles QM: Convergence, convergence, convergence

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

Further Study

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


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.

Synopsis

Introduction to the Mesoscale

  • Techniques
  • Physical scales
  • Mesoscale simulation strategies

Dissipative Particle Dynamics (DPD)

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

Lattice Boltzmann Equation (LBE)

  • 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

Simulation of Organic and Bio Molecules


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.

Synopsis

Introduction

  • Biomolecules
  • Molecular Dynamics Software
  • Force Fields for Biomolecules

Set-up / Analysis

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

Enhanced Sampling

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

Nucleic Acids

  • DNA

Multiscale Modelling

  • QM/MM
  • Coarse-graining
  • Code Coupling

Free Energy Methods

  • Ligand Binding
  • FEP
  • Alchemical Perturbations

Campus Maps


to be added soon