institute for computational biomedicine: CHARMM

[ description ]

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for performing molecular dynamics and mechanics computations. CHARMM may be used for energy minimization, normal mode analysis, chemical and conformational free energy analysis, and a variety of other computations as well. The force field typically used with CHARMM is parameterized for proteins, nucleic acids and lipids.

[ documentation ]

The CHARMM 28b2 documentation is available from the CHARMM web site. A good deal of CHARMM information is also available from the Brooks Lab web page.

[ availability ]

Both serial and parallel versions of CHARMM 28b2 are available on all IRIX computers, and on osiris and isis. The IRIX builds use CHARMM's large configuration option; the builds on osiris and isis use CHARMM's xxlarge configuration.

After you have configured your account to use WMC login scripts, you can use the charmm command at the UNIX command prompt to run the serial version of CHARMM.

Example:

$ charmm < input_file.inp > output_file.out

To run a parallel version of CHARMM, use the charmm_mpi2, charmm_mpi4, or charmm_mpi8 commands.

Example:

$ charmm_mpi4 < input_file.inp > output_file.out

A charmm directory can be found at /usr/global/opt/any/pkg/charmm_28b2_data. This directory contains parameter files (in toppar) that you may wish to copy or refer to in your CHARMM jobs as well as a local copy of the documentation (in doc). Executables are not found in this directory.

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]

Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301