Molecular modeling and simulation (AP403001)

This course in intended for PhD students who have not attended course M403002.
It contains only necessary statistical thermodynamics, but more simulations; otherwise, the overlap with M403002 is large.

• Česká verze přednášky pro Mgr úroveň
• Částečně česká verze pro PhD úroveň (Pokročilé metody a Molekulární modelování a simulace)
• English versions for PhD level (Advanced methods of MD and and Molecular modeling and simulation):
  The talks marked by + are extended in the advanced course.
• Extended syllabus

Links

• Molecular modelling and simulation (taught in English at Technical University of Liberec): older local version with movies
• SIMOLANT, free software for teaching molecular dynamics and Monte Carlo

Talks

# lecture for print (10:1) 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 8+ Structural quantities simen08.10.pdf 9 System size, potential range, Coulomb forces simen09.10.pdf 10 More ensembles: MC simen10.10.pdf 11 More ensembles: MD simen11.10.pdf 12 Non-Boltzmann sampling, constraint dynamics, optimization simen12.10.pdf 13+ Brownian dynamics, DPD, kinetic quantities, EMD vs. NEMD simen13.10.pdf

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