CHARMM

Description

charmm website  

CHARMM (Chemistry at HARvard Macromolecular Mechanics):

• is a versatile and widely used molecular simulation program with broad application to many-particle systems
• 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
• 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
• is useful for a much broader class of many-particle systems
• 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
• has been ported to numerous platforms in both serial and parallel architectures

Variants

• CHARMM 35b2
• CHARMM 36a3

Execution Environment and Modules

To use charmm with the environment modules system at HPC the following commands are available:

Get module information for charmm:

$module spider charmm

Load the default application module:

$module load charmm

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_CHARMM_DIR - directory where charmm is located.

How To Run

Note that the parallel version of CHARMM seems to not accept input redirection and looked for "charmm.inp" even after placing "-i my_input.inp" on the command line. This is the reason for the symlink of "charmm.inp" to the actual input file in the sample script.

Configuration

See the CHARMM_Configuration page for charmm configuration details.

PBS Script Examples

See the CHARMM_PBS page for charmm PBS script examples.