520028 VU Advanced molecular simulation: free energies, enhanced sampling and rare events (2023S)
Continuous assessment of course work
Labels
Registration/Deregistration
Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).
- Registration is open from We 01.02.2023 08:00 to Th 23.02.2023 07:00
- Deregistration possible until Fr 31.03.2023 23:59
Details
max. 15 participants
Language: English
Lecturers
Classes (iCal) - next class is marked with N
- Tuesday 07.03. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 09.03. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 14.03. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 16.03. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 21.03. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 23.03. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 28.03. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 30.03. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 18.04. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 20.04. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 25.04. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 27.04. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 02.05. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 04.05. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 09.05. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 11.05. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 16.05. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 23.05. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 25.05. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 01.06. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 06.06. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 13.06. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 15.06. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
- Tuesday 20.06. 09:45 - 11:15 Seminarraum 9, Kolingasse 14-16, OG01
- Thursday 22.06. 11:30 - 13:00 Seminarraum 9, Kolingasse 14-16, OG01
Information
Aims, contents and method of the course
Assessment and permitted materials
There wil be a final written exam at the end of the semester. The exercises will be continuously assessed based on uploaded notebooks and presentations of solved exercises in class.
Minimum requirements and assessment criteria
The final exam and the continuous assessment will contribute equally to the final grade. More details will be provided in the first lecture.
Examination topics
All topics discussed in the lectures and exercises.
Reading list
J. Hénin, T. Lelièvre, M. R. Shirts, O. Valsson and L. Delemotte, "Enhanced Sampling Methods for Molecular Dynamics Simulations", Living Journal of Computational Molecular Science, 4, 1583 (2022).
https://doi.org/10.33011/livecoms.4.1.1583Christoph Dellago and Peter G. Bolhuis , "Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events". Adv. Polym. Sci. 221, 167-233 (2008).
https://doi.org/10.1007/978-3-540- 87706-6_3.B. Smit and D. Frenkel, "Understanding Molecular Simulation: From Algorithms to Applications", Academic Press (2001)B. Peters, "Reaction Rate Theory and Rare Events", Elsevier (2017).
https://www.elsevier.com/books/reaction-rate-theory- and-rare-events/peters/978-0-444-56349-1.M. Tuckerman, "Statistical Mechanics: Theory and Molecular Simulation", Oxford University Press (2010)
https://doi.org/10.33011/livecoms.4.1.1583Christoph Dellago and Peter G. Bolhuis , "Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events". Adv. Polym. Sci. 221, 167-233 (2008).
https://doi.org/10.1007/978-3-540- 87706-6_3.B. Smit and D. Frenkel, "Understanding Molecular Simulation: From Algorithms to Applications", Academic Press (2001)B. Peters, "Reaction Rate Theory and Rare Events", Elsevier (2017).
https://www.elsevier.com/books/reaction-rate-theory- and-rare-events/peters/978-0-444-56349-1.M. Tuckerman, "Statistical Mechanics: Theory and Molecular Simulation", Oxford University Press (2010)
Association in the course directory
M-VAF A 2, M-VAF B
Last modified: Th 02.03.2023 14:49
- Thermodynamic integration
- Free energy perturbation
- Umbrella sampling
- WHAM, BAR and MBAR
- Replica exchange
- Adaptive bias methods: Wang-Landau sampling and metadynamics
- Additional topics*: non-equilibrium methods, Nested sampling, temperature accelerated MDIII. Kinetics of rare events
- What is the rare event problem? Reaction rate constants, time correlation functions, etc.
- Transition state theory, Kramers theory
- Reactive flux method
- Transition path sampling
- Identifying the mechanism: the committor
- Transition path theory and the string method (nudged elastic band)
- Additional topics: forward flux sampling, milestoning, seeding for nucleation, accelerated MD*Additional topics will be discussed depending on the available time and interests of the participants