Difference between revisions of "Advanced sampling techniques and atomistic modeling"
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| − | + | Group leader: [[Kai Kratzer]] | |
| + | Members: {{#ask:[[Topical Meeting::sampling]]}} | ||
| − | + | In this topical group, we discuss advanced / meta sampling techniques. We concentrate on two main problems, namely the sampling of rare transitions and free energies. | |
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| − | ''' | + | == Schedule == |
| + | The meeting takes place every three weeks on '''Tuesdays at 10:30''', if not indicated differently. | ||
| − | + | === WS 2014/2015 === | |
| + | * Tue, '''02.12.2014''': Progress reports | ||
| + | * Tue, '''11.11.2014''': Rare event sampling with FFS, SPRES and FRESHS. Introduction of the work of the new group members | ||
| + | * Tue, '''21.10.2014''': Initial meeting WS 2014/2015, progress reports | ||
| − | Tue, '''17. | + | === SS 2014 === |
| + | * Tue, '''9.9.2014''': Progress reports | ||
| + | * Tue, '''19.8.2014''': Progress reports | ||
| + | * Tue, '''29.7.2014''': Progress reports | ||
| + | * Tue, '''08.07.2014''': Progress reports | ||
| + | * Tue, '''17.06.2014''': Progress reports | ||
| + | * Tue, '''27.05.2014''': Progress reports | ||
| + | * Tue, '''06.05.2014''': Progress reports | ||
| + | * Tue, '''15.04.2014''': Progress reports | ||
| − | Tue, '''15.10.2013''': Introduction (JZ, ET), progress report | + | === WS 2013/2014 === |
| + | * Tue, '''25.03.2014 (10:00)''': Progress reports, short presentations of the advanced sampling contributions for the DPG spring meeting. | ||
| + | * Tue, '''04.03.2014''': Progress reports and crystallization of charged macromolecules as rare event (KK) | ||
| + | * Tue, '''04.02.2014''': Progress report (JZ), Calculating surface tension and chemical potential (TK) | ||
| + | * Tue, '''21.01.2014''': Progress report (ET), FFS using automatic, optimized interface placement (KK) | ||
| + | * Tue, '''07.01.2014''': Progress report (TK), Umbrella Sampling, Metadynamics (JM, JL) | ||
| + | * Tue, '''10.12.2013''': Progress report (JL), Parallel FFS simulations, statistics backtracking, decorrelation and efficient simulation control (KK,JZ) | ||
| + | * Tue, '''26.11.2013''': Progress report (JM), FRESHS: The Flexible Rare Event Sampling Harness System (KK) | ||
| + | * Tue, '''12.11.2013''': Progress report (KK), free energy landscapes and stationary distributions (JZ) | ||
| + | * Tue, '''29.10.2013''': Progress report (TK, KK), order parameters / reaction coordinates / collective variables (ET) | ||
| + | * Tue, '''15.10.2013''': Introduction (JZ, ET), progress report (JZ) | ||
| + | * Tue, '''17.09.2013''': Initial meeting & introduction (KK, TK, JL, JM) | ||
| − | + | == Tools == | |
| + | For rare events, we use | ||
| + | * Forward Flux Sampling | ||
| + | * Transition Interface Sampling | ||
| + | The standard tool here is [http://freshs.org FRESHS] | ||
| − | + | For free energy calculations | |
| − | + | * Umbrella Sampling | |
| − | + | * Metadynamics | |
| − | + | The standard tool here is [http://plumed-code.org PLUMED] | |
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Latest revision as of 13:05, 2 December 2014
Group leader: Kai Kratzer Members: Angel Diaz Carral, Ewa Anna Oprzeska-Zingrebe, Fabian Zills, Maria Fyta, Samuel Tovey
In this topical group, we discuss advanced / meta sampling techniques. We concentrate on two main problems, namely the sampling of rare transitions and free energies.
Schedule
The meeting takes place every three weeks on Tuesdays at 10:30, if not indicated differently.
WS 2014/2015
- Tue, 02.12.2014: Progress reports
- Tue, 11.11.2014: Rare event sampling with FFS, SPRES and FRESHS. Introduction of the work of the new group members
- Tue, 21.10.2014: Initial meeting WS 2014/2015, progress reports
SS 2014
- Tue, 9.9.2014: Progress reports
- Tue, 19.8.2014: Progress reports
- Tue, 29.7.2014: Progress reports
- Tue, 08.07.2014: Progress reports
- Tue, 17.06.2014: Progress reports
- Tue, 27.05.2014: Progress reports
- Tue, 06.05.2014: Progress reports
- Tue, 15.04.2014: Progress reports
WS 2013/2014
- Tue, 25.03.2014 (10:00): Progress reports, short presentations of the advanced sampling contributions for the DPG spring meeting.
- Tue, 04.03.2014: Progress reports and crystallization of charged macromolecules as rare event (KK)
- Tue, 04.02.2014: Progress report (JZ), Calculating surface tension and chemical potential (TK)
- Tue, 21.01.2014: Progress report (ET), FFS using automatic, optimized interface placement (KK)
- Tue, 07.01.2014: Progress report (TK), Umbrella Sampling, Metadynamics (JM, JL)
- Tue, 10.12.2013: Progress report (JL), Parallel FFS simulations, statistics backtracking, decorrelation and efficient simulation control (KK,JZ)
- Tue, 26.11.2013: Progress report (JM), FRESHS: The Flexible Rare Event Sampling Harness System (KK)
- Tue, 12.11.2013: Progress report (KK), free energy landscapes and stationary distributions (JZ)
- Tue, 29.10.2013: Progress report (TK, KK), order parameters / reaction coordinates / collective variables (ET)
- Tue, 15.10.2013: Introduction (JZ, ET), progress report (JZ)
- Tue, 17.09.2013: Initial meeting & introduction (KK, TK, JL, JM)
Tools
For rare events, we use
- Forward Flux Sampling
- Transition Interface Sampling
The standard tool here is FRESHS
For free energy calculations
- Umbrella Sampling
- Metadynamics
The standard tool here is PLUMED