Difference between revisions of "Advanced sampling techniques and atomistic modeling"

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Group leader: [[Kai Kratzer]]
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Members: {{#ask:[[Topical Meeting::sampling]]}}
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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.
 
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 ==
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The meeting takes place every three weeks on '''Tuesdays at 10:30''', if not indicated differently.
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=== WS 2014/2015 ===
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* Tue, '''02.12.2014''': Progress reports
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* Tue, '''11.11.2014''': Rare event sampling with FFS, SPRES and FRESHS. Introduction of the work of the new group members
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* Tue, '''21.10.2014''': Initial meeting WS 2014/2015, progress reports
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=== SS 2014 ===
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* Tue, '''9.9.2014''': Progress reports
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* Tue, '''19.8.2014''': Progress reports
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* Tue, '''29.7.2014''': Progress reports
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* Tue, '''08.07.2014''': Progress reports
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* Tue, '''17.06.2014''': Progress reports
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* Tue, '''27.05.2014''': Progress reports
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* Tue, '''06.05.2014''': Progress reports
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* Tue, '''15.04.2014''': Progress reports
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=== WS 2013/2014 ===
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* Tue, '''25.03.2014 (10:00)''': Progress reports, short presentations of the advanced sampling contributions for the DPG spring meeting.
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* Tue, '''04.03.2014''': Progress reports and crystallization of charged macromolecules as rare event (KK)
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* Tue, '''04.02.2014''': Progress report (JZ), Calculating surface tension and chemical potential (TK)
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* Tue, '''21.01.2014''': Progress report (ET), FFS using automatic, optimized interface placement (KK)
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* Tue, '''07.01.2014''': Progress report (TK), Umbrella Sampling, Metadynamics (JM, JL)
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* Tue, '''10.12.2013''': Progress report (JL), Parallel FFS simulations, statistics backtracking, decorrelation and efficient simulation control (KK,JZ)
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* Tue, '''26.11.2013''': Progress report (JM), FRESHS: The Flexible Rare Event Sampling Harness System (KK)
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* Tue, '''12.11.2013''': Progress report (KK), free energy landscapes and stationary distributions (JZ)
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* Tue, '''29.10.2013''': Progress report (TK, KK), order parameters / reaction coordinates / collective variables (ET)
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* Tue, '''15.10.2013''': Introduction (JZ, ET), progress report (JZ)
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* Tue, '''17.09.2013''': Initial meeting & introduction (KK, TK, JL, JM)
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== Tools ==
 
For rare events, we use
 
For rare events, we use
 
* Forward Flux Sampling
 
* Forward Flux Sampling
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* Metadynamics
 
* Metadynamics
 
The standard tool here is [http://plumed-code.org PLUMED]
 
The standard tool here is [http://plumed-code.org PLUMED]
 
''' Group members:'''
 
 
      Kai Kratzer (KK) (group leader)
 
      Tarun Khanna (TK)
 
      Evangelos Ribeiro Tzaras (ET)
 
      Julian Michalowsky (JM)
 
      Jonas Landsgesell (JL)
 
      Johannes Zeman (JZ)
 
 
''' Schedule '''
 
 
Every meeting will start at '''10:30''' if not indicated differently.
 
 
Tue, '''17.09.2013''': Initial meeting & introduction (KK, TK, JL, JM)
 
 
Tue, '''15.10.2013''': Introduction (JZ, ET), progress report
 
 
Tue, '''29.10.2013''': Progress report, order parameters / reaction coordinates / collective variables
 
 
Tue, '''12.11.2013''': Progress report, free energy landscapes and stationary distributions
 
 
Tue, '''26.11.2013''': Progress report, Umbrella Sampling
 
 
Tue, '''10.12.2013''': Progress report, Metadynamics
 
 
Tue, '''14.01.2014''': Progress report, Forward Flux Sampling using automatic, optimized interface placement (KK)
 
 
Tue, '''28.01.2014''': Progress report, Classical Nucleation Theory
 
 
Tue, '''11.02.2014''': Progress report, Calculating surface tension and chemical potential (cleaving wall and particle insertion method) (TK)
 

Latest revision as of 13:05, 2 December 2014

Group leader: Kai Kratzer Members: Ewa Anna Oprzeska-Zingrebe, Johannes Zeman, Maria Fyta, Takeshi Kobayashi

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