Molecular modeling and simulation (AP40301)
Advanced methods for molecular dynamics (AP403005)
The courses are in English or Czech, according to the audience (česká verze)
About
- Course Molecular modeling and simulation (AP40301) is intended for PhD
students who did not attend the simulation part of Mgr
course Statistická
termodynamika, molekulové modelování a simulace. In covers basics
of modeling, MC and MD methods, and to some extend more advanced
parts. It is tought by Jiří Kolafa.
- Course Advanced methods for molecular dynamics is composed of two parts:
- prof. RNDr. Jiří Kolafa, CSc.: Advanced second part of the previous course with extensions.
- RNDr. Mgr. Jan Heyda, PhD.: Kirkwood–Buff theory, polymers, metadynamics etc.
Links
Talks by J. Kolafa
Symbol “+” in column # means that the talk contains additional material
in comparison with the Molecular modeling and simulation level/
| # |
Talk in PDF |
For print (10:1) |
Movie |
|---|
| 0 |
Popular introduction |
simen00.10.pdf |
| 1 |
Statistical thermodynamics |
simen01.10.pdf |
| 2 |
Models, force field |
simen02.10.pdf |
| 3+ |
Molecular dynamics; Verlet (and some theoretical mechanics) |
simen03.10.pdf |
| 4+ |
Gear methods, thermostats in MD (w/o Nosé-Hoover) |
simen04.10.pdf |
| 5 |
Monte Carlo, random numbers |
simen05.10.pdf |
| 6 |
Simulation methodology, errors |
simen06.10.pdf |
| 7+ |
Measuring thermodynamic quantities |
simen07.10.pdf |
Entropic quantities (metadynamics, histogram reweighting) (52:41) |
| 8+ |
Structural quantities |
simen08.10.pdf |
| 9 |
System size, potential range, Coulomb forces |
simen09.10.pdf |
| 10+ |
More ensembles: MC |
simen10.10.pdf |
Fluctuations, finite-size effects (20:58)
MC in various ensembles (35:03) |
| 11+ |
More ensembles: MD |
simen11.10.pdf |
| 12+ |
Non-Boltzmann sampling, constraint dynamics, optimization |
simen12.10.pdf |
Hastings algorithm, force-bias, preferential sampling (13:23) |
| 13+ |
Brownian dynamics, DPD, kinetic quantities, EMD vs. NEMD | simen13.10.pdf |
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