CHARMM

CHARMM models the dynamics and mechanics of macromolecular systems using empirical and mixed empirical/quantum mechanical force fields.

CHARMM is designed to investigate the structure and dynamics of large molecules. It performs free energy calculations of mutations and drug binding as well as conformational folding of peptides. It uses classical mechanical methods to investigate potential energy surfaces derived from experimental and "ab initio" quantum chemical calculations. In addition, mixed quantum mechanical/classical systems can be defined to investigate chemical processes such as enzyme catalysis.

Available for: blacklight and salk.

However, access to CHARMM is restricted. You must have an academic license for CHARMM to use it on PSC systems. To get a license, see below.

Setting up CHARMM

You must install CHARMM for you own use. To do so, follow these steps:

  1. Obtain an academic license for CHARMM.

    Access to CHARMM is restricted. You must have an academic license for CHARMM to use it on PSC systems. To get a license, contact:

    Professor Martin Karplus
    Department of Chemistry & Chemical Biology
    Harvard University
    12 Oxford Street
    Cambridge, MA 02138
    Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

  2. Copy the CHARMM code to blacklight or salk.

    CHARMM code is provided with the license. When you have obtained an academic license, copy the CHARMM code into your directory.

  3. Copy the PSC install script to your directory.
    • On blacklight, copy /usr/local/packages/charmm/install_charmm_uv into the directory where the CHARMM install.com script is located.
    • On salk, copy /usr/local/packages/charmm_install/install_charmm_4700 into your directory where the CHARMM install.com script is located.
  4. Run the PSC install script
    • On blacklight, from the directory containing both the CHARMM install.com script and the PSC install script:
      ./install_charmm_uv
      .
    • On salk, from the directory containing both the CHARMM install.com script and the PSC install script:
      ./install_charmm_4700

Using CHARMM

Once you have installed CHARMM, the executable will be in your directory tree.

  • On blacklight, the executable is /exec/em64t/charmm under the installation directory.
  • On salk, the executable is /exec/altix/charmm under the installation directory.

To run CHARMM:

  1. Create a job script containing a line similar to
     mpirun -np $PBS_NCPUS path-to-executable/charmm < input > output
    
  2. Submit the job script with the qsub command.
Last Updated on Wednesday, 07 December 2011 11:34  

More on CHARMM

Reference: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, Journal of Computational Chemistry,4, 187-217 (1983) by B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus.

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