Difference between revisions of "Category:Tutorials"

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This page contains all the tutorials which should help you get using Avogadro efficiently.
 
This page contains all the tutorials which should help you get using Avogadro efficiently.
  
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Here is an incomplete list of tutorials which need to be written:
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{| align="left" style="border-spacing:8px;margin:0px -8px"
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# [[Tutorials:Getting started]] (opening files, docks, settings (quality), navigation,  ...)
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|-
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# [[Tutorials:Drawing molecules]] (draw tool, hydrogens extension, cartesian editor, quick optimization (using defaults), ...)
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| width="50%" class="MainPageBG" style="border: 1px solid #FFC435; background-color: #f8fff8; vertical-align:top;"|
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# [[Tutorials:Making selections]] (needed for engine tutorial, more details about what you can do with a selection (delete, copy/paste, explain that certain tools/extension operate on selections, ...)
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<h3 style="background:#FFC435;margin:-2px;padding:4px;"> ''Step-By-Step Walkthroughs'' </h3>
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# [[Tutorials:Engines]] (selecting, enabling, configuring)
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<div style="padding: 2px 10px 6px;">
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# [[Tutorials:Orbitals]] (orbital engine/extension)
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# [[Tutorials:Using the bond centric tool]]
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* [[Tutorials:Getting started]]
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# [[Tutorials:Molecular mechanics]] (force field extension, AutoOpt tool)
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: Opening files, navigation, render settings
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# [[Tutorials:Advanced molecular mechanics]] (using constraints to make cyclohexane go from chair to boat, ...)
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* [[Tutorials:Drawing molecules]]
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: Drawing, adding/removing hydrogens, editing atom coordinates, geometry optimization
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* [[Tutorials:Making selections]]
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: Delete, copy/paste, operating on selections
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* [[Tutorials:Display Types]]
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: Selecting, enabling, configuring how molecules are displayed
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* [[Tutorials:Altering Bonds]]
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: Changing bond length, angles, and dihedrals
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* [[Tutorials:Orbitals]]
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: Viewing output from quantum chemistry programs
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* [[Tutorials:Insert SMILES]]
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: Drawing structures with a SMILES string
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* [[Tutorials:Insert a Peptide]]
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: Drawing and editing peptide structures
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* [[Tutorials:Crystal Unit Cells]]
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: Working with crystals
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* [[Tutorials:Molecular Mechanics]]
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: AutoOptimize, optimize geometry, and friends
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* [[Tutorials:Force fields]]
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: Which force field to use, commonly made mistakes, tips, etc.
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* [[Tutorials:Advanced molecular mechanics]]
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: Using constraints
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* [[Tutorials:Console]]
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: Manipulating molecules in Avogadro, using the Python console
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</div>
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| width="50%" class="MainPageBG" style="border: 1px solid #FFC435; background-color: #f8fff8; vertical-align:top;"|
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<h3 style="background:#FFC435;margin:-2px;padding:4px;"> ''Video Tutorials'' </h3>
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<div style="padding: 2px 10px 6px;">
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* [http://home.scarlet.be/timvdm/navigate.htm Opening files and navigation (3.5MB)]
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* [http://home.scarlet.be/timvdm/drawing.htm Drawing (3.3MB)]
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* [http://home.scarlet.be/timvdm/display.htm Working with display types (26MB)]
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Some [[screencasts]] also are useful as tutorials.
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</div>
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<h3 style="background:#FFC435;margin:-2px;padding:4px;"> ''Advanced Walk-Throughs'' </h3>
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<div style="padding: 2px 10px 6px;">
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* [[Tutorials:Polymer Unit Cell]]
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: Building a polythiophene unit cell for Gaussian (or other) calculation.
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* [http://www.d.umn.edu/~psiders/courses/chem4642/quantumchemsoftware/tutorial/avogadro/avogadro.html Avogadro for P-Chem Lab]
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: Building molecules with Avogadro for GAMESS-US calculations.
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* [http://molecularmodelingbasics.blogspot.com/search/label/avogadro Molecular Modeling Basics]
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: Tutorials for Avogadro from Jan Jensen's Molecular Modeling Basics blog
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* [http://www.redbrick.dcu.ie/~noel/GAMESS_Apr2011/index.html Introduction to GAMESS]
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: Running GAMESS-US calculations with Avogadro
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</div>
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|}
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<css>
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#mw-pages { display: none; }
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</css>
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[[Category:Documentation]]

Latest revision as of 11:20, 17 May 2012

This page contains all the tutorials which should help you get using Avogadro efficiently.

Step-By-Step Walkthroughs

Opening files, navigation, render settings
Drawing, adding/removing hydrogens, editing atom coordinates, geometry optimization
Delete, copy/paste, operating on selections
Selecting, enabling, configuring how molecules are displayed
Changing bond length, angles, and dihedrals
Viewing output from quantum chemistry programs
Drawing structures with a SMILES string
Drawing and editing peptide structures
Working with crystals
AutoOptimize, optimize geometry, and friends
Which force field to use, commonly made mistakes, tips, etc.
Using constraints
Manipulating molecules in Avogadro, using the Python console

Video Tutorials

Advanced Walk-Throughs

Building a polythiophene unit cell for Gaussian (or other) calculation.
Building molecules with Avogadro for GAMESS-US calculations.
Tutorials for Avogadro from Jan Jensen's Molecular Modeling Basics blog
Running GAMESS-US calculations with Avogadro


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