Difference between revisions of "Simulationsmethoden II SS2010"

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== Overview ==
 
== Overview ==
−
==Simulationsmethoden in der Physik I:Simulation Methods in Physics I ==
+
==Simulationsmethoden in der Physik II: Simulation Methods in Physics II ==
  
 
;Type
 
;Type
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:Prof. Dr. [[Christian Holm]] (Lecture) and  [[Joan Josep Cerdà]],  [[Nadezhda Gribova]] (Tutorials)
 
:Prof. Dr. [[Christian Holm]] (Lecture) and  [[Joan Josep Cerdà]],  [[Nadezhda Gribova]] (Tutorials)
 
;Course language
 
;Course language
−
:English
+
:English or German, depending on audience
 
;Time and Room
 
;Time and Room
−
:Lecture times:  Monday, 11:30 a.m.-1 p.m., Room V27.03
+
:Lecture times:  Wednesday, 9:45 a.m.-11:15 pa.m., V27.03,  Pfaffenwaldring 27
 
:Tutorial times: Wednesday, 3:30 p.m.-5:30 p.m., Room U 108 (Pfaffenwaldring 27)
 
:Tutorial times: Wednesday, 3:30 p.m.-5:30 p.m., Room U 108 (Pfaffenwaldring 27)
 
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.
 
The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.
−
The tutorials build on each other, therefore continuous attendance is expected.
+
The tutorials build on each other, therefore continuous attendance is expected. The solutions to the worksheet will be handed in and graded,
  
 
==Scope==
 
==Scope==
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lecture will consist of:
 
lecture will consist of:
  
−
'''1. '''
+
'''1. ''' Biomolecular Simulation Approaches
  
−
'''2. '''
+
'''2. ''' Coarse Graining Strategies for Soft Matter
  
−
'''3. '''
+
'''3. ''' Efficient Methods for Treating Long Range Interactions
  
−
'''4. '''
+
'''4. ''' Free Energy Calculations
 +
 
 +
'''5. ''' Advanced Monte Carlo Methods
  
 
== Prerequisites ==
 
== Prerequisites ==
 
We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).
 
We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).
 +
The successful attendence of the previous course Simulation methods I is required, since we will build up the lecture on previously gained knowledge.
  
 
== Certificate Requirements:==
 
== Certificate Requirements:==
 +
There will be a final grade for the Modul "Simulation Methods" determined at the end of this course.
 +
 +
The final grade will be determined in the following way :
  
−
The final mark would consists :
+
:1. 50% comes from  the marks for the hand-in exercises for ''' both''' parts of the course (Simulation Methods in Physics I and II)
 +
These are determined by the best marks obtained in 6 out of 7 tutorials in Sim I plus all accumulated marks of all 6 tutorials in Sim II.
  
−
:1. 50% of the marks for the hand-in exercises (attendance of the exercise classes is required)
+
:2. 50% will be determined in an  oral examination performed at (or after) the end of the course.
−
:2. 50% of the mark at the oral exam in the end of the course.
 
  
  
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!Date !! Subject
 
!Date !! Subject
 
|-
 
|-
−
| 19.04.10 ||  
+
|-21.04.10 || Intro to ''in silicio'' Biology
 
|-
 
|-
−
| 26.04.10 ||  
+
| 28.04.10 || Ab-initio QM Methods
 
|-
 
|-
−
| 03.05.10 ||  
+
| 05.05.10 || DFT Methods, Water models
 
|-
 
|-
−
| 10.05.10 ||  
+
| 12.05.10 || Born Model, Simulating Macromolecules
 
|-
 
|-
−
| 17.05.10 ||  
+
| 19.05.10 || Implicit Solvent Model, Bead-Spring Model
 
|-
 
|-
−
| 31.05.10 ||  
+
| 02.06.10 || Coarse-grained models for macromolecules
 
|-
 
|-
−
| 07.06.10 ||  
+
| 09.06.10 || Treating long-range interaction in periodic geometries, <br>Introduction to Poisson-Boltzmann theory
 
|-
 
|-
−
| 14.06.10 ||  
+
| 16.06.10 || Poisson-Boltzmann theory, polyelectrolytes and charged colloids {{Download|Lecture7.pdf|PDF}} <br> also look at    ''M. Deserno and C. Holm: [http://www.ica1.uni-stuttgart.de/~icp/bib/pdf/icp/deserno01c.pdf Cell-model and Poisson-Boltzmann-theory: <br>A brief introduction]''
 
|-
 
|-
−
| 21.06.10 ||  
+
| 23.06.10 || Hydrodynamic Interactions: Brownian Dynamics, Lattice-Boltzmann Methods
 
|-
 
|-
−
| 28.06.10 ||  
+
| 30.06.10 || Dissipative Particle Dynamics
 
|-
 
|-
−
| 05.07.10 ||  
+
| 07.07.10 || Free Energy Calculations
 
|-
 
|-
−
| 12.07.10 ||  
+
| 14.07.10 || Advanced Monte Carlo Simulations: Parallel Tempering
 
|-
 
|-
−
| 19.07.10 ||  
+
| 21.07.10 || Advanced Monte Carlo Simulations: Reweighting
 
|-
 
|-
 
|}
 
|}
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!Date !! Subject
 
!Date !! Subject
 
|-
 
|-
−
|21.04/28.04 || Error Analysis.
+
|21.04/28.04 || [[Error Analysis.]]
 
|-
 
|-
 
|05.05/12.05 || Atomistic simulations using GROMACS package. Water models.
 
|05.05/12.05 || Atomistic simulations using GROMACS package. Water models.

Latest revision as of 14:23, 28 July 2010

Overview

Simulationsmethoden in der Physik II: Simulation Methods in Physics II

Type
Lecture (2 SWS) and Tutorials (1 SWS)
Lecturer
Prof. Dr. Christian Holm (Lecture) and Joan Josep Cerdà, Nadezhda Gribova (Tutorials)
Course language
English or German, depending on audience
Time and Room
Lecture times: Wednesday, 9:45 a.m.-11:15 pa.m., V27.03, Pfaffenwaldring 27
Tutorial times: Wednesday, 3:30 p.m.-5:30 p.m., Room U 108 (Pfaffenwaldring 27)

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis. The tutorials build on each other, therefore continuous attendance is expected. The solutions to the worksheet will be handed in and graded,

Scope

The course intends to give an overview about modern simulation methods used in physics today. The stress of the lecture will be to introduce different approaches to simulate a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:

1. Biomolecular Simulation Approaches

2. Coarse Graining Strategies for Soft Matter

3. Efficient Methods for Treating Long Range Interactions

4. Free Energy Calculations

5. Advanced Monte Carlo Methods

Prerequisites

We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++). The successful attendence of the previous course Simulation methods I is required, since we will build up the lecture on previously gained knowledge.

Certificate Requirements:

There will be a final grade for the Modul "Simulation Methods" determined at the end of this course.

The final grade will be determined in the following way :

1. 50% comes from the marks for the hand-in exercises for both parts of the course (Simulation Methods in Physics I and II)

These are determined by the best marks obtained in 6 out of 7 tutorials in Sim I plus all accumulated marks of all 6 tutorials in Sim II.

2. 50% will be determined in an oral examination performed at (or after) the end of the course.


Lecture

Date Subject
28.04.10 Ab-initio QM Methods
05.05.10 DFT Methods, Water models
12.05.10 Born Model, Simulating Macromolecules
19.05.10 Implicit Solvent Model, Bead-Spring Model
02.06.10 Coarse-grained models for macromolecules
09.06.10 Treating long-range interaction in periodic geometries,
Introduction to Poisson-Boltzmann theory
16.06.10 Poisson-Boltzmann theory, polyelectrolytes and charged colloids application_pdf.pngPDF (6.08 MB)Info circle.png
also look at M. Deserno and C. Holm: Cell-model and Poisson-Boltzmann-theory:
A brief introduction
23.06.10 Hydrodynamic Interactions: Brownian Dynamics, Lattice-Boltzmann Methods
30.06.10 Dissipative Particle Dynamics
07.07.10 Free Energy Calculations
14.07.10 Advanced Monte Carlo Simulations: Parallel Tempering
21.07.10 Advanced Monte Carlo Simulations: Reweighting

Tutorials (U 108)

Date Subject
21.04/28.04 Error Analysis.
05.05/12.05 Atomistic simulations using GROMACS package. Water models.
19.05/02.06 Introduction to ESPResSo package. Simulation of a polymer.
16.06/23.06 Simulation of a charged rod.
30.06/07.07 Lattice Bolzmann.
14.07/21.07 Advanced MD.

Recommended literature

  • Daan Frenkel, Berend Smit.
    Understanding Molecular Simulation: From Algorithms to Applications.
    Part of Computational Science, volume 1. Edition 2.
    Academic Press, San Diego, 2002. ISBN: 978-0-12-267351-1.
    [DOI]
  • Mike P. Allen, Dominik J. Tildesley.
    Computer Simulation of Liquids.
    Part of Oxford Science Publications. Edition 1.
    Clarendon Press, Oxford, 1987.
  • D. C. Rapaport.
    The Art of Molecular Dynamics Simulation.
    Edition 2.
    Cambridge University Press, 2004. ISBN: 9780511816581.
    [DOI]
  • D. P. Landau, K. Binder.
    A guide to Monte Carlo Simulations in Statistical Physics.
    Edition second edition.
    Cambridge, 2005.
  • M. E. J. Newman, G. T. Barkema.
    Monte Carlo Methods in Statistical Physics.
    Edition 2002 edition.
    Oxford University Press, 1999.
  • H. J. Limbach, A. Arnold, B. A. Mann, C. Holm.
    ESPResSo – An Extensible Simulation Package for Research on Soft Matter Systems.
    Computer Physics Communications 174(9):704–727, 2006.
    [PDF] (318 KB) [DOI]


Available E-Books

D.P. Landau and K. Binder.

"A guide to Monte Carlo Simulations in Statistical Physics"

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