CHARMM

Policy

CHARMM is available to users at HPC2N under the condition that they acquire a licence for it by contacting The CHARMM Development Project. Read more about how to do that here. When you (or your PI) have acquired a license you should contact support@hpc2n.umu.se with the information. You will then be given access to using CHARMM.

General

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. 

Description

CHARMM has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments.

It provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities and it is useful for a much broader class of many-particle systems.

CHARMM can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models.

It has been ported to numerous platforms in both serial and parallel architectures.

Availability

On HPC2N we have CHARMM available as a module on Akka.

Usage at HPC2N

To use the charmm module, add it to your environment:

module add charmm

Loading the module should set all the needed environmental variables as well as the path. 

It is possible to run CHARMM  interactively, but it is not the recommended way, except for graphics.

The general syntax for using the program 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.

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.

Additional info

Documentation is available on the CHARMM documentation page.