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.

Installed on: Big Ben, pople and salk.

Access to CHARMM is restricted. Follow these instructions to obtain access.

Big Ben

  • Version 32b1
  • Executables reside in /usr/local/packages/CHARMM-c32b1. They are:
    • charmm
    • charmm321xl_mpi
  • Submit a batch job containing a line similar to: 
     pbsyod charmm  < input > output
  • Consult the bigben documentation for more information about submitting a job.
  • Example job.

CHARMM on Pople

Version c34b2

Private versions installed on Pople

If you install your own version of CHARMM on pople, there are two lines in install.com which must be modified.

  1. Look for the line: 
    else if ( $chmhost == altix ) then
        set BLAS=-lscs_i8
    and change it to: 
    else if ( $chmhost == altix ) then
        set BLAS=-lmkl
  2. Look for the line: 
    case altix:
   if (! -e prefx_altix ) efc -static -o prefx_$$  prefx.f
    and change it to: 
    case altix:
   if (! -e prefx_altix ) ifort -static -o prefx_$$  prefx.f

The second one is the most important since it tells CHARMM to use the ifort compiler instead of efc. efc is not installed on Pople.

CHARMM on Salk

Version c34b2

  • Executable is /usr/local/packages/charmm/c34b2/exec/altix/charmm.
  • Submit a batch job containing a line similar to: 
    mpirun -np $PBS_NCPUS /usr/local/packages/charmm/c34b2/exec/altix/charmm  <input  >  output
  • Consult the salk documentation for more information on submitting jobs.
  • Example job