CHARMM - Revision history

import>Csw34 at 10:16, 30 April 2008

2008-04-30T10:16:13Z

← Older revision		Revision as of 10:16, 30 April 2008
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	== Tutorials ==		== Tutorials ==
			* [[input file basics]] - the bare minimum you need to include!
	* [[converting between '.crd' and '.pdb']]		* [[converting between '.crd' and '.pdb']]
	* [[calculating molecular properties]] - i.e. energy, rgyr etc		* [[calculating molecular properties]] - i.e. energy, rgyr etc

import>Csw34 at 14:13, 29 April 2008

2008-04-29T14:13:09Z

← Older revision		Revision as of 14:13, 29 April 2008
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	CHARMM is a program capable of running all or united atom energy minimization, Molecular Dynamics and Monte Carlo simulations. We don't often use CHARMM on its own, but rather use it through the interface to [[OPTIM]] and [[GMIN]]. There are however a few occasions when you can use CHARMM itself to calculate useful properties i.e. energy, radius of gyration, rmsd from a reference structure, or you might want to convert between ''.crd'' and ''.pdb'' formats. CHARMM can do all these things for you if you give it the correct input. Below are detailed a few of the most useful features of CHARMM. If you want to find out more about what else you can do, search the documentation, preferably on one of the clusters in the ''doc'' directory or online [http://www.charmm.org/html/documentation/c32b2/index.html here]. This is for a more recent version of the code but you should be able to find what you need.		[http://www.charmm.org CHARMM] (Chemistry at HARvard Macromolecular Mechanics) is a program capable of running all or united atom energy minimization, Molecular Dynamics and Monte Carlo simulations. We don't often use CHARMM on its own, but rather use it through the interface to [[OPTIM]] and [[GMIN]]. There are however a few occasions when you can use CHARMM itself to calculate useful properties i.e. energy, radius of gyration, rmsd from a reference structure, or you might want to convert between ''.crd'' and ''.pdb'' formats. CHARMM can do all these things for you if you give it the correct input. Below are detailed a few of the most useful features of CHARMM. If you want to find out more about what else you can do, search the documentation, preferably on one of the clusters in the ''doc'' directory or online [http://www.charmm.org/html/documentation/c32b2/index.html here]. This is for a more recent version of the code but you should be able to find what you need.

	== Tutorials ==		== Tutorials ==
	* [[converting between ''.crd'' and ''.pdb'']]		* [[converting between '.crd' and '.pdb']]
	* [[calculating molecular properties]] - i.e. energy, rgyr etc		* [[calculating molecular properties]] - i.e. energy, rgyr etc
	* [[loops and variables in CHARMM]]		* [[loops and variables in CHARMM]]

import>Csw34 at 14:11, 29 April 2008

2008-04-29T14:11:59Z

New page

CHARMM is a program capable of running all or united atom energy minimization, Molecular Dynamics and Monte Carlo simulations. We don't often use CHARMM on its own, but rather use it through the interface to [[OPTIM]] and [[GMIN]]. There are however a few occasions when you can use CHARMM itself to calculate useful properties i.e. energy, radius of gyration, rmsd from a reference structure, or you might want to convert between ''.crd'' and ''.pdb'' formats. CHARMM can do all these things for you if you give it the correct input. Below are detailed a few of the most useful features of CHARMM. If you want to find out more about what else you can do, search the documentation, preferably on one of the clusters in the ''doc'' directory or online [http://www.charmm.org/html/documentation/c32b2/index.html here]. This is for a more recent version of the code but you should be able to find what you need.

== Tutorials ==
* [[converting between ''.crd'' and ''.pdb'']]
* [[calculating molecular properties]] - i.e. energy, rgyr etc
* [[loops and variables in CHARMM]]
* [[using CHARMM to orient molecules at the origin]]
* [[atom selection in CHARMM]] - including the .around. syntax for spatial selection