Computational Chemistry Toolkit

2010-09-03T13:00:07Z

Documentation of the Packages:

←Older revision		Revision as of 13:00, 3 September 2010
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	* GROMACS (MD Simulation Tool): [http://www.gromacs.org Main Page], [http://www.gromacs.org/Documentation Documentation], [http://md.chem.rug.nl/education/mdcourse/ Tutorial], [http://oldwww.gromacs.org/ Old Gromacs]		* GROMACS (MD Simulation Tool): [http://www.gromacs.org Main Page], [http://www.gromacs.org/Documentation Documentation], [http://md.chem.rug.nl/education/mdcourse/ Tutorial], [http://oldwww.gromacs.org/ Old Gromacs]
	* GROMACS 3.3: [[Media:Manual-3.3.pdf\|Paper Manual]]		* GROMACS 3.3: [[Media:Manual-3.3.pdf\|Paper Manual]]
-	* GROMACS 4.5 (newest version): [http://www.gromacs.org/index.php?title=Download_%26_Installation New Version GROMACS 4.5 ~~beta 3~~] (mainly GPU computing support, many bugs already fixed),	+	* GROMACS 4.5 (newest version): [http://www.gromacs.org/index.php?title=Download_%26_Installation New Version GROMACS 4.5.1] (mainly GPU computing support, many bugs already fixed),
-	[http://www.gromacs.org/Documentation/Manual Manual GROMACS 4.5 beta 2], [http://manual.gromacs.org/current/ Online References]	+	[http://www.gromacs.org/Documentation/Manual Manual GROMACS 4.5 beta 2], [http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5 New Features], [http://manual.gromacs.org/current/ Online References]
	* PLEASE NOTE: The GROMACS website has been renewed but it is still under construction.		* PLEASE NOTE: The GROMACS website has been renewed but it is still under construction.
	* Hence, the links of the tools which are new in GROMACS 4.0 do not work yet.		* Hence, the links of the tools which are new in GROMACS 4.0 do not work yet.
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	* Molden (Display Molecular Density): [http://www.cmbi.ru.nl/molden/ Main Page], [http://www.cmbi.ru.nl/molden/opengl.html OpenGL: gmolden], New: [http://www.cmbi.ru.nl/molden/ambfor.html Optimization by Amber Force Field (ambfor)], [http://www.cmbi.ru.nl/molden/ambforc.html ambfor for Small Protein Complexes], [http://www.cmbi.ru.nl/molden/HISTORY New Version: Molden 4.9]		* Molden (Display Molecular Density): [http://www.cmbi.ru.nl/molden/ Main Page], [http://www.cmbi.ru.nl/molden/opengl.html OpenGL: gmolden], New: [http://www.cmbi.ru.nl/molden/ambfor.html Optimization by Amber Force Field (ambfor)], [http://www.cmbi.ru.nl/molden/ambforc.html ambfor for Small Protein Complexes], [http://www.cmbi.ru.nl/molden/HISTORY New Version: Molden 4.9]
	* Moscito (MD Simulation Tool): [http://ganter.chemie.uni-dortmund.de/MOSCITO/ Main Page], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_man.html Manual], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_mosview.html Mosview (Trajectory Viewer)], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_downl.html New: Moscito 4.170]		* Moscito (MD Simulation Tool): [http://ganter.chemie.uni-dortmund.de/MOSCITO/ Main Page], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_man.html Manual], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_mosview.html Mosview (Trajectory Viewer)], [http://ganter.chemie.uni-dortmund.de/MOSCITO/moscito_downl.html New: Moscito 4.170]
-	* LAMMPS (MD Simulation Tool): [http://lammps.sandia.gov/ Main Page], [http://lammps.sandia.gov/doc/Manual.html Online Documentation], [http://lammps.sandia.gov/bug.html#15Jan10 New commands or new options on existing commands], New in LAMMPS: [http://lammps.sandia.gov/doc/pair_comb.html Charge-Optimized Many-Body (COMB) potential] and its [http://lammps.sandia.gov/doc/fix_qeq_comb.html Charge-Equilibration Procedure], suitable for a variety of metals and semiconductors and their oxides	+	* LAMMPS (MD Simulation Tool): [http://lammps.sandia.gov/ Main Page], [http://lammps.sandia.gov/doc/Manual.html Online Documentation], [http://lammps.sandia.gov/bug.html#15Jan10 New commands or new options on existing commands],
		+	New in LAMMPS:
		+	* [http://lammps.sandia.gov/doc/pair_eff.html Electron Force Field (EFF)] for modeling of electrons
		+	* [http://lammps.sandia.gov/doc/pair_eim.html Embedded Ion Potential (EIM)] for modeling of ionic compounds
		+	* [http://lammps.sandia.gov/doc/pair_comb.html Charge-Optimized Many-Body (COMB) potential] and its [http://lammps.sandia.gov/doc/fix_qeq_comb.html Charge-Equilibration Procedure], suitable for a variety of metals and semiconductors
		+	and their oxides
	* GAMESS (QC Package): [http://www.msg.ameslab.gov/GAMESS/ Main Page], [http://www.msg.ameslab.gov/GAMESS/documentation.html Online Documentation], [http://www.msg.ameslab.gov/tutorials/tutorials.html Online Tutorials], [http://www.msg.ameslab.gov/advances/updatepaper.html New Features]		* GAMESS (QC Package): [http://www.msg.ameslab.gov/GAMESS/ Main Page], [http://www.msg.ameslab.gov/GAMESS/documentation.html Online Documentation], [http://www.msg.ameslab.gov/tutorials/tutorials.html Online Tutorials], [http://www.msg.ameslab.gov/advances/updatepaper.html New Features]
	* RED-III (Charge Derive Tool): [http://q4md-forcefieldtools.org/RED/ Main Page], [http://q4md-forcefieldtools.org/RED/RED-II.pdf Manual (Version II.0)], [http://q4md-forcefieldtools.org/Tutorial/ Tutorials], [http://q4md-forcefieldtools.org/RED/release34.php New Version: III.4], [http://q4md-forcefieldtools.org/RED/HowTo-III.4.pdf HowToUse Version III.4]		* RED-III (Charge Derive Tool): [http://q4md-forcefieldtools.org/RED/ Main Page], [http://q4md-forcefieldtools.org/RED/RED-II.pdf Manual (Version II.0)], [http://q4md-forcefieldtools.org/Tutorial/ Tutorials], [http://q4md-forcefieldtools.org/RED/release34.php New Version: III.4], [http://q4md-forcefieldtools.org/RED/HowTo-III.4.pdf HowToUse Version III.4]

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Computational Chemistry Toolkit