Difference between revisions of "Template:Free Energy Howto"

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{{sidebar with collapsible lists
 
{{sidebar with collapsible lists
 
| expanded      = {{{cTopic}}}
 
| expanded      = {{{cTopic}}}
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| name          = Fundamentals
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| name          = Free Energy Howto
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| title          = Free Energy Fundamentals
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| title          = Free Energy How-to's
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| image          = [[file:Transformation_small.png|frameless]]
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| image          = [[file:ligandtranslate.png|frameless]]
 
| caption        =  
 
| caption        =  
  
 
| content1      =  
 
| content1      =  
  
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| list2name      = Theory
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| list2name      = Examples
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| list2title    = '''[[Free Energy Fundamentals | Theory]]'''
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| list2title    = '''[[Example Free Energy Calculations | Example Calculations]]'''
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| list2          = [[Definitions]]<br/>[[Exponential Averaging|Exponential Averaging / Zwanzig]]<br/>[[Thermodynamic Integration]]<br/>[[Bennett Acceptance Ratio]]<br/>[[Weighted Histogram Analysis Method | Weighted Histogram Analysis]]<br/>[[Multistate Bennett Acceptance Ratio|MBAR]]<hr/>
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| list2          = [[Example: Absolute Solvation Free Energy| Absolute Solvation Free Energy]] <br/> [[Example: Relative Binding Affinity | Relative Binding Affinity]] <br/> [[Example: Absolute Binding Affinity |Absolute Binding Affinity]] <hr/>
  
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| list3name      = Methods
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| list3name      = Tutorials
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| list3title    = '''Methods of Free Energy Simulations'''
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| list3title    = '''[[Tutorials]]'''
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| list3          = [[Thermodynamic Cycle]]<br/>[[Intermediate States]] ([[Intermediate States#Constructing Intermediate States|Constructing]]) <br/> [[Intermediate States#Soft Core Potentials | Soft Core Potentials]] <br/> [[Simulating States of Interest | Running Simulations]]<br/>[[Simulation Information Gathering|Extracting Simulation Information]]<br/>[[Analyzing Simulation Results|Analysis]] / [[Analyzing Simulation Results#Bootstrap Sampling | Bootstrap Sampling]]<hr/>
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| list3          = [[GROMACS 4.6 example: Direct ethanol solvation free energy | Ethanol Solvation - GROMACS]] <br/> [[GROMACS 4.6 example: Ethanol solvation with expanded ensemble | Expanded Ensemble - GROMACS]][[Category:Free Energy How-to's]] <br/> [[Absolute Binding Free Energy - Gromacs 2016 | Absolute Binding Free Energy - GROMACS]]}}
  
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| list4name      = Acceleration
 
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| list4title    = '''[[Simulation Acceleration | Improving Sampling and Accelerating Simulations]]'''
 
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| list4          = [[Simulation Acceleration#Umbrella Sampling | Umbrella Sampling]]<br/> [[Simulation Acceleration#Hamiltonian Replica Exchange | Hamiltonian Replica Exchange]]<br/>[[Simulation Acceleration#Other Methods | <math>\lambda</math>-dynamics]] / [[Simulation Acceleration#Other Methods | Expanded Ensemble]]
 
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| list5name      = Examples
 
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| list5title    = '''[[Example Free Energy Calculations | Examples]]'''
 
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| list5          = [[Example: Absolute Solvation Free Energy| Absolute Solvation Free Energy]] <br/> [[Example: Relative Binding Affinity | Relative Binding Affinity]] <br/> [[Example: Absolute Binding Affinity |Absolute Binding Affinity]]}}[[Category:Free Energy How-to's]]
 
  
 
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Latest revision as of 06:32, 23 March 2017

Free Energy How-to's
Ligandtranslate.png


This infobox is done in the style as the Thermodynamics Infobox Template from Wikipedia.

This box contains the How tos and the Examples sections

Retrieved from "http://alchemistry.org/wiki/index.php?title=Template:Free_Energy_Howto&oldid=3014"