Difference between revisions of "CHARMm"

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'''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.
 
'''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 ==
+
==Syntax==
* [http://en.wikipedia.org/wiki/CHARMm Wikipedia article on '''CHARMm''']
+
The general syntax for using the program is:
* [http://www.accelrys.com/ Accelrys website]
+
 
* [http://www.charmm.org/ CHARMM website]
+
charmm < filename.inp > filename.out
* [http://www.scripps.edu/brooks/ C.Brooks website]
+
 
* [http://yuri.harvard.edu/ Harvard page]
+
; <tt>charmm</tt> : The actual name of the program (or script which runs the program) on the computer system being used.
* [http://thallium.med.cornell.edu/RouxLab/ Roux website]
+
; <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.
* [http://www.pharmacy.umaryland.edu/faculty/amackere/ MacKerell website]
+
 
 +
; <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==
 +
*[http://www.charmm.org/ CHARMM 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.accelrys.com/ Accelrys 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]
 +
*[[wikipedia:CHARMm]]
  
 
{{stub}}
 
{{stub}}
[[Category:Technical and Specialized Skills]]
+
[[Category:Bioinformatics]]

Latest revision as of 00:49, 3 April 2009

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.

Syntax

The general syntax for using the program is:

charmm < filename.inp > filename.out
charmm 
The actual name of the program (or script which runs the program) on the computer system being used.
filename.inp 
A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and 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.
filename.out 
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

External links

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