Molecular modeling and simulation (česká verze)

Info

Homework:
1. Coding a MD simulation of a harmonic oscillator, see simen04, pp. 9–10
2. Either coding a MC of a molecule in a gravitational field, see simen05, p. 14
  or determining the value of π by the Buffon needle method, see simen05, pp. 2–3
Simulation project: choose here, or as negotiated
Extended syllabus
The exam consists of:
- Written test from Statistical Thermodynamics (by A. Malijevsky)
- Short written test from Modeling and Simulation
- Oral exam.
  In case of good results in the written tests and the project, the oral part may be skipped.
Grade:
- 0.5*(statmech)+0.3*(simulation test)+0.1*(homework)+0.1*(project)

#	lecture	for print (8:1)
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