Difference between revisions of "CHARMm"
From Christoph's Personal Wiki
(Started article) |
|||
| (One intermediate revision by the same user not shown) | |||
| 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. | '''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 | + | The commercial version of CHARMM, called '''CHARMm''' (note the lowercase 'm'), is available from Accelrys. |
| − | == | + | ==Syntax== |
| − | + | The general syntax for using the program is: | |
| − | * [http://www. | + | |
| − | * [http://www. | + | 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] — 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: | + | [[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.
Contents
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
- Newton's equation of motion
- Newton's Second Law of motion
- Integration algorithms
External links
- CHARMM website
- MD tutorial — provides a theoretical introduction to molecular dynamics simulations and practical examples using the CHARMM program.
- Accelrys website
- C.Brooks website
- Harvard page
- Roux website
- MacKerell website
- wikipedia:CHARMm
This article is curently a "stub". This means it is an incomplete article needing further elaboration.
I always welcome suggestions, comments, and criticism. If you have something to contribute to this site, please follow this link: Contributing Information. Thank you!
