CHarMM c32b2

CHARMM Development and Information

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids. Free energy methods for chemical and conformational free energy calculations are also fully developed and available in CHARMM. Many other novel tools have been developed and are available in CHARMM, these include: replicas (multiple copies); many types of restraints and constraints, including fixed atoms, atomic, NOE, dihedral and internal coordinate restraints and generalized SHAKE for bonds and arbitrary internal coordinates; minimium energy path following and transition state optimization; etc.

CHARMM development began in the research group of Professor Martin Karplus at Harvard University. Development continues throughout the world with contributing developers in over 20 universities, research institutes and companies. CHARMM is available to academic users in full source form, plus extensive documentation and test input scripts, through Harvard University. A license for CHARMM can be obtained by inquiring to:

Professor Martin Karplus
Department of Chemistry & Chemical Biology
Harvard University
12 Oxford Street
Cambridge, MA 02138
(Contact Martin Karplus)

The appropriate references for CHARMM in publications are:

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

CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, 1, 271-277, P. v. R. Schleyer et al., editors (John Wiley & Sons: Chichester, 1998), by A. D. MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus.

from http://brooks.chem.lsa.umich.edu/charmm_docs/charmm.htm

Usage

If you wish to test your input file before submitting production jobs to PBS you should start by:

module load charmm

charmm < filename.inp > & filename.out [[param:value] ...] [ & ]

where:

charmm: The actual name of the program (or script which runs the program) on the computer system being used
filename.inp: A text file containing CHARMM input commands, using the command syntax described in usage.doc. The filename is up to the user.
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

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.

-from http://brooks.chem.lsa.umich.edu/charmm_docs/c32docs/c32a1/

Remember that a run on the head node must complete within 5 minutes; so you'll need to run your production codes from PBS.

As before start with:

module load charmm

Then submit a script, such as the one below,

qsub ex.scr

#PBS -N charmm_test #PBS -q route #PBS -l nodes=2:ppn=2,walltime=24:00:00 #PBS -S /bin/csh #PBS -M your-email-address #PBS -m abe #PBS -V # echo "I ran on:" cat $PBS_NODEFILE # #cd to your execution directory first cd /home/your-user-name # mpirun -np 4 $chmroot/exec/gnu/charmm < $chmroot/test/c28test/gridtest.inp #

however if your input file to charm contains a goto you should use the following form of PBS script.

#PBS -N charmm_test #PBS -q route #PBS -l nodes=2:ppn=2,walltime=24:00:00 #PBS -S /bin/csh #PBS -M your-email-address #PBS -m abe #PBS -V # echo "I ran on:" cat $PBS_NODEFILE # #cd to your execution directory first cd /home/your-user-name # echo "* CHARMM test stream file for parallel runs" >stream.inp echo "* where rewinding stdin is not possible" >>stream.inp echo "stream @stream" >>stream.inp echo "stop" >>stream.inp echo $chmroot mpirun -np 4 $chmroot/exec/gnu/charmm stream=$chmroot/test/c28test/gridtest.inp



About the CAC Academics Getting Started Getting Help FAQ Resources Current Outages No outages have been reported Planned Outages No outages have been scheduled Search The CAC	CHarMM c32b2 CHARMM Development and Information CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids. Free energy methods for chemical and conformational free energy calculations are also fully developed and available in CHARMM. Many other novel tools have been developed and are available in CHARMM, these include: replicas (multiple copies); many types of restraints and constraints, including fixed atoms, atomic, NOE, dihedral and internal coordinate restraints and generalized SHAKE for bonds and arbitrary internal coordinates; minimium energy path following and transition state optimization; etc. CHARMM development began in the research group of Professor Martin Karplus at Harvard University. Development continues throughout the world with contributing developers in over 20 universities, research institutes and companies. CHARMM is available to academic users in full source form, plus extensive documentation and test input scripts, through Harvard University. A license for CHARMM can be obtained by inquiring to: Professor Martin Karplus Department of Chemistry & Chemical Biology Harvard University 12 Oxford Street Cambridge, MA 02138 (Contact Martin Karplus) The appropriate references for CHARMM in publications are: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations, J. Comp. Chem. 4, 187-217 (1983), by B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, 1, 271-277, P. v. R. Schleyer et al., editors (John Wiley & Sons: Chichester, 1998), by A. D. MacKerell, Jr., B. Brooks, C. L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. from http://brooks.chem.lsa.umich.edu/charmm_docs/charmm.htm Usage If you wish to test your input file before submitting production jobs to PBS you should start by: module load charmm charmm < filename.inp > & filename.out [[param:value] ...] [ & ] where: charmm The actual name of the program (or script which runs the program) on the computer system being used filename.inp A text file containing CHARMM input commands, using the command syntax described in usage.doc. The filename is up to the user. 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 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. -from http://brooks.chem.lsa.umich.edu/charmm_docs/c32docs/c32a1/ Remember that a run on the head node must complete within 5 minutes; so you'll need to run your production codes from PBS. As before start with: `module load charmm` Then submit a script, such as the one below, qsub ex.scr `#PBS -N charmm_test #PBS -q route #PBS -l nodes=2:ppn=2,walltime=24:00:00 #PBS -S /bin/csh #PBS -M your-email-address #PBS -m abe #PBS -V # echo "I ran on:" cat $PBS_NODEFILE # #cd to your execution directory first cd /home/your-user-name # mpirun -np 4 $chmroot/exec/gnu/charmm < $chmroot/test/c28test/gridtest.inp #` however if your input file to charm contains a goto you should use the following form of PBS script. #PBS -N charmm_test #PBS -q route #PBS -l nodes=2:ppn=2,walltime=24:00:00 #PBS -S /bin/csh #PBS -M your-email-address #PBS -m abe #PBS -V # echo "I ran on:" cat $PBS_NODEFILE # #cd to your execution directory first cd /home/your-user-name # echo "* CHARMM test stream file for parallel runs" >stream.inp echo "* where rewinding stdin is not possible" >>stream.inp echo "stream @stream" >>stream.inp echo "stop" >>stream.inp echo $chmroot mpirun -np 4 $chmroot/exec/gnu/charmm stream=$chmroot/test/c28test/gridtest.inp