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CHARMM
 
CHARMM
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 runs on Linux machines s; the executable is in:

/joule2/programs/charmm/c28b2/exec/gnu/charmm  or just type "charmm"

The local documentation is in:

/joule2/programs/charmm/c28b2/support/htmldoc/Overview_generic.Html

or from the author's web site at

http://www.scripps.edu/mb/brooks/charmm_docs/c28docs/c28b2/ 

also see the users document files at:
/joule2/programs/charmm/c28b2/doc

ace.doc          charmm_gen.doc   energy.doc       hbonds.doc       mc.doc           nmr.doc          qmmm.doc         support.doc
adumb.doc        charmmrate.doc   ewald.doc        hbuild.doc       minimiz.doc      nose.doc         replica.doc      test.doc
analys.doc       commands.doc     flucq.doc        hqbm.doc         miscom.doc       parallel.doc     rism.doc         testcase.doc
aspenr.doc       cons.doc         fourd.doc        images.doc       mmff.doc         parmfile.doc     rtop.doc         travel.doc
block.doc        corman.doc       galgor.doc       install.doc      mmff_params.doc  pbeq.doc         sbound.doc       umbrel.doc
cadpac.doc       correl.doc       gamess-uk.doc    intcor.doc       mmfp.doc         pdetail.doc      scalar.doc       usage.doc
cff.doc          crystl.doc       gamess.doc       io.doc           molvib.doc       pert.doc         select.doc       vibran.doc
cfti.doc         developer.doc    genborn.doc      lonepair.doc     monitor.doc      perturb.doc      shapes.doc
changelog.doc    dynamc.doc       graphx.doc       lupopt.doc       mts.doc          pimplem.doc      struct.doc
charmm.doc       eef1.doc         grid.doc         mbond.doc        nbonds.doc       pressure.doc     subst.doc


Charlotte Deane's helpful perl scripts will allow you to run CHARMM in
a fairly painless fashion if you are working on simple problems.

see /joule2/programs/charmm/c28b2/perlscripts