Scope
The documentation presented here is that for the latest academic version of the CHARMM program (Chemistry at HARvard Molecular Mechanics). The information in these .doc files has been contributed by CHARMM developers over the years, and hopefully reflects the current state of the program. The Harvard designation for this version is c33b1, where "c" refers to CHARMM, 33 is the version number and the letters "b" or "a" indicate the release, i.e. beta or alpha. Note that beta level codes are distribution version to CHARMM users and alpha level codes are development versions.CHARMM remains essentially a command line program, i.e. a command is read from the input stream (typed, or from a file) and acted upon. In fact, several parts of CHARMM are under active development, and there are often significant enhancements since the previous versions were released. Consequently, there will be periodic changes and additions to the documentation offered here.
Running CHARMM Under Unix
While CHARMM may be run interactively, that is not usually recommended, except for graphics; even then, a stream file should be used for the initial setup (reading PSF, coords, etc.). The general syntax for using the program (assuming /bin/csh) is:charmm [[param:value] ...] < filename.inp > filename.out &
- charmm
- The actual name of the program (or script which runs the program) on the computer system being used; the name may not be the same on all systems.
- filename.inp
- A text file containing CHARMM input commands, using the command syntax described in usage.doc. The actual filename is up to the user, although it is useful to use short names which hint at the overall purpose, e.g. makpsf.inp
- 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.
- param:value
- CHARMM script parameters (essentially user defined variables) may optionally be defined on Unix shell command line, using the form param:value; the value is substituted for occurrences of @param in the input script.
- &
- The optional ampersand will place the program in the background under most Unix shells; note that the computer system being used may have a batch job queueing system which should normally be used instead of running CHARMM as a background process via the above syntax.
Consult the local system administrator to determine the actual program name (e.g. charmm, charmm24, etc.) and the policy for running compute intensive tasks (batch queue, background, etc.) on the computer system being used. In general, CHARMM calculations are best limited to around 24 to 48 hours, to both promote resource sharing and to minimize data loss due to machine or network failures.
