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

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(Created page with "''' Group members:''' Kai Kratzer (KK) (group leader) Tarun Khanna (TK) Evangelos Ribeiro Tzaras (ET) Julian Michalowsky (JM) Jonas Landsgesell ...")
 
 
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''' Group members:'''
+
Group leader: [[Kai Kratzer]]
 +
Members: {{#ask:[[Topical Meeting::sampling]]}}
  
      Kai Kratzer (KK) (group leader)
+
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.
      Tarun Khanna (TK)
 
      Evangelos Ribeiro Tzaras (ET)
 
      Julian Michalowsky (JM)
 
      Jonas Landsgesell (JL)
 
      Johannes Zeman (JZ)
 
  
''' Schedule '''
+
== Schedule ==
 +
The meeting takes place every three weeks on '''Tuesdays at 10:30''', if not indicated differently.
  
Every meeting will start 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, '''17.09.2013''': Initial meeting & introduction (KK, TK, JL, JM)
+
=== 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)
  
Tue, '''29.10.2013''': Progress report, order parameters / reaction coordinates / collective variables
+
== Tools ==
 +
For rare events, we use
 +
* Forward Flux Sampling
 +
* Transition Interface Sampling
 +
The standard tool here is [http://freshs.org FRESHS]
  
Tue, '''12.11.2013''': Progress report, free energy landscapes and stationary distributions
+
For free energy calculations
 
+
* Umbrella Sampling
Tue, '''26.11.2013''': Progress report, Umbrella Sampling
+
* Metadynamics
 
+
The standard tool here is [http://plumed-code.org PLUMED]
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