Overview of CHARMM vers. c24n5 .doc Files
Scope
The documentation presented here is that for the latest academic
version of the CHARMM program (Chemistry at HARvard Molecular
Mechanics), as maintained at the NIH development site. Quite a few
features are contained in this version that are NOT included in the
CHARMm version distributed by Biosym-MSI as part of the
Quanta package. 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 c24b1, indicating the first beta release of CHARMM version 24; the NIH version (c24n5) may contain a few bugfixes and other minor differences relative to the c24b1 release.
The compiled program itself is available on several computer systems at NIH, and
this documentation is largely meant as an on-line usage guide for people
using CHARMM on these systems. At present it is more of a reference manual
than a tutorial, although in the coming months material from the CHARMM
lectures previously presented by BR Brooks (DCRT/LSB) will be added to these WWW pages.
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. Even the X11 graphics function this way, although that part may change
over the next year or so. In fact, several parts of CHARMM are under
active development, and there are significant enhancements since the previous version (c23) was 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 < filename.inp >& filename.out [[param:value] ...] [ & ]
- 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 12 to 16 hours, to both promote resource sharing and to minimize data loss due to machine or network failures.
For foreground usage, e.g. graphics, start the program by typing it's name
alone, wait for the program "header" to be printed, and enter a title.
Then use a "stream" file, e.g.
stream psf-crd.str
will read CHARMM commands from the file named psf-crd.str as if they
were being typed at the keyboard; as implied by the name, the stream file
reads the PSF, PARAms, COORdinates, etc., the basic starting point for all
work with CHARMM.
Information and HTML pages provided by:
NIH/DCRT Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Documentation Overview / rvenable@deimos.cber.nih.gov