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The presentations are in English. Optional (not compulsory) parts are marked orange and/or + sign.
- Read and report a scientific paper in the
field of molecular modeling and simulation. You can choose either a
paper from the list (see the link below), or any paper from the broad field of
modeling/simulations of your own choice.
In the latter case, please send me the paper first. See http://old.vscht.cz/fch/tresen/Predmet2.html for more information.
- Write a final test and score at least 50%. A sample test is given below.
- In case of marginal results, an oral exam may follow.
- Read and report a scientific paper in the field of molecular modeling and simulation. You can choose either a paper from the list (see the link below), or any paper from the broad field of modeling/simulations of your own choice. In the latter case, please send me the paper first. See http://old.vscht.cz/fch/tresen/Predmet2.html for more information.
Popular introduction to modeling in chemistry and simulation with examples.
- Microcanonical ensemble and the ergodic hypothesis
- Canonical ensemble and Boltzmann probability
- Thermodynamics and the Boltzmann equation for entropy
- Optional: isobaric and grand-canonical ensembles
Models + exercises
1. Model hierarchy
2. Atom-atom interactions
3. Force field in molecular modeling
4. Construction of force fields
5. External forces
6. Lattice models
Molecular dynamics – the Verlet method
- Newton equations of motion
- Verlet method
- Leap-frog method and its equivalence to the Verlet method
- Show: planet revolution
- Velocity Verlet
Other methods, temperature in MD
- Optional: Gear methods
- Temperature in MD
• based on the Maxwell-Boltzmann distribution
• based on velocity rescaling (Berendsen method)
• Nosé-Hoover method (qualitatively)
• workout: thermostats in SIMOLANT (see below for the installation of SIMOLANT)
Monte Carlo methods
Monte Carlo methods
- Naive Monte Carlo
- Metropolis method
- Markov chains
- Acceptance ratio
Workout: comparison of MC and MD using SIMOLANT
Simulation methodology and workout 1
- Pseudoexperiment – start, equilibration, measurement
- Boundary conditions
- Errors of correlated time series
- Mechanical quantities: temperature, internal energy, pressure
- Entropic quantities (thermodynamic integration, Widom, integrating reversible work, local density method)
- Verify the Clausius–Clapeyron equation by simulations of a 2D model of matter
Structural quantities and workout 2
- Radial distribution function
- Experiment: structure factor and RDF
- RDF from simulations
- Workout: molecular dynamics (simenw2.pdf):
- melting point of NaCl in the slab geometry;
- structure of water around a solute;
- coalescence of two water droplets.
Short and long range forces
- Short-range forces: cutoff, correction
- Electrostatic forces: smooth cutoff; Ewald summation; reaction field (qualitatively)
- MC of rigid models
- In brief: optimization, parallel code
SIMOLANT - Computer simulations of phase transitions