CHARMm - Revision history

Christoph at 00:49, 3 April 2009

2009-04-03T00:49:51Z

Christoph at 01:02, 5 May 2007

2007-05-05T01:02:32Z

Christoph: Started article

2006-05-21T13:43:38Z

Started article

New page

'''CHARMM''' ('''Chemistry at HARvard Macromolecular Mechanics''') is a force field for molecular dynamics as well as the name for the molecular dynamics simulation package associated with this force field. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.

The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm') is available from [[Accelrys]].

== External links ==
* [http://en.wikipedia.org/wiki/CHARMm Wikipedia article on '''CHARMm''']
* [http://www.accelrys.com/ Accelrys website]
* [http://www.charmm.org/ CHARMM website]
* [http://www.scripps.edu/brooks/ C.Brooks website]
* [http://yuri.harvard.edu/ Harvard page]
* [http://thallium.med.cornell.edu/RouxLab/ Roux website]
* [http://www.pharmacy.umaryland.edu/faculty/amackere/ MacKerell website]

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[[Category:Technical and Specialized Skills]]

← Older revision		Revision as of 00:49, 3 April 2009
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	The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm'), is available from Accelrys.		The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm'), is available from Accelrys.
		+
		+	==Syntax==
		+	The general syntax for using the program is:
		+
		+	charmm < filename.inp > filename.out
		+
		+	; <tt>charmm</tt> : The actual name of the program (or script which runs the program) on the computer system being used.
		+	; <tt>filename.inp</tt> : A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and [[Force field (chemistry)\|force field]] (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files). One can then modify the molecules (adding hydrogens, changing secondary structure). The calculation section can include energy minimization, dynamics production, and analysis tools such as motion and energy correlations.
		+
		+	; <tt>filename.out</tt> : The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications. The values for temperature, energy pressure, etc. are output at that frequency.
		+
		+	==Data structures==
		+	===Topology and Parameter Files===
		+
		+	====Residue Topology File (RTF)====
		+	*Example of the RTF for the Alanine residue:
		+	RESI ALA0.00
		+	GROUP
		+	ATOM NNH1-0.47 ! \|
		+	ATOM HNH 0.31 ! HN-N
		+	ATOM CACT1 0.07 ! \| HB1
		+	ATOM HAHB 0.09 ! \| /
		+	GROUP !HA-CA--CB-HB2
		+	ATOM CBCT3-0.27 ! \| \
		+	ATOM HB1HA 0.09 ! \| HB3
		+	ATOM HB2HA 0.09 ! O=C
		+	ATOM HB3HA 0.09 ! \|
		+	GROUP !
		+	ATOM CC 0.51
		+	ATOM OO-0.51
		+	BONDCB CA N HN N CA
		+	BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
		+	DOUBLE O C
		+	IMPR N -C CA HN C CA +N O
		+	DONOR HN N
		+	ACCEPTOR O C
		+	IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
		+	IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
		+	IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
		+	IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
		+	IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
		+	IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
		+	IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
		+	IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
		+	IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
		+	IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
		+
		+	;Parameter File (PARAM) : see "Lennard-Jones 6-12 potential parameters"
		+	;Protein Structure File (PSF) :
		+	;Coordinate File (CRD) :
		+	;Internal Coordinate Table (IC Table) :
		+
		+	==Statistical mechanics==
		+	===Keywords / concepts===
		+	*ensemble
		+	*Calculating averages from a molecular dynamics simulation
		+	*Ergodic hypothesis
		+	*Average potential energy
		+	*Average kinetic energy
		+
		+	==Classical mechanics==
		+	===Keywords / concepts===
		+	*[[wikipedia:Equations of motion\|Newton's equation of motion]]
		+	*Newton's Second Law of motion
		+	*Integration algorithms
		+	**[[wikipedia:Leapfrog integration\|Leapfrog integration]]
		+	**[[wikipedia:Newmark-beta method\|Newmark-beta method]]
		+	**[[wikipedia:Verlet integration\|Velocity Verlet]]
		+	**[[wikipedia:Beeman's algorithm\|Beeman's algorithm]]

	==External links==		==External links==

@@ Line 1: / Line 1: @@
 '''CHARMM''' ('''Chemistry at HARvard Macromolecular Mechanics''') is a force field for molecular dynamics as well as the name for the molecular dynamics simulation package associated with this force field. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
-The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm') is available from [[Accelrys]].
+The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm'), is available from Accelrys.
-== External links ==
+==External links==
-* [http://en.wikipedia.org/wiki/CHARMm Wikipedia article on '''CHARMm''']
+*[http://www.charmm.org/ CHARMM website]
-* [http://www.accelrys.com/ Accelrys website]
+*[http://www.ch.embnet.org/MD_tutorial/ MD tutorial] &mdash; provides a theoretical introduction to molecular dynamics simulations and practical examples using the CHARMM program.
-* [http://www.charmm.org/ CHARMM website]
+*[http://www.accelrys.com/ Accelrys website]
-* [http://www.scripps.edu/brooks/ C.Brooks website]
+*[http://www.scripps.edu/brooks/ C.Brooks website]
-* [http://yuri.harvard.edu/ Harvard page]
+*[http://yuri.harvard.edu/ Harvard page]
-* [http://thallium.med.cornell.edu/RouxLab/ Roux website]
+*[http://thallium.med.cornell.edu/RouxLab/ Roux website]
-* [http://www.pharmacy.umaryland.edu/faculty/amackere/ MacKerell website]
+*[http://www.pharmacy.umaryland.edu/faculty/amackere/ MacKerell website]
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-[[Category:Technical and Specialized Skills]]
+[[Category:Bioinformatics]]