Subject: CCL:GPL'd (and friends) MM/QM packages :: Summary

From: Avijit Ghosh <[email-masked]>
Date: Tue, 20 Mar 2001 14:10:14 -0500 (EST)

Wow the GPL discussion has popped up again. I asked something
a bit similiar to this tread a few months ago and compiled a list of
packages that seemed related.  The series of packages eventually evolved
into a  bit beyond GPL'd  into the more general "Source available"
packages.

There are two corrections from the original post : (1) I mistakenly called
David Case's NAB  GPLish rather than GPL and (2) B (Java based MD) whose
license is actually "less restrictive" than GPL rather than unknown.  I've
deleted  all the original responses for brevity this time but I am sure
they are in  the archives somewhere..

	Regards,
	-avi

------

I've extracted out the links into a compiled list as well as included
the responses as a whole below that for some of the details w/ regards
to particular programs. I've also added a few descriptors etc etc..

Here is the original question :
--------------------original message----------------------------------

	I was wondering whether anyone has any GPL'd code for MD?
 Particularly, whether there are any GPL'd force field
implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a
package (MOIL) here that is more or less public domain which includes an
Amber88/(soon to be 95 implementation). There  are a series of
very nice programs that are available with source (NAMD/VMD  from UIUC),
Tinker from wustl (which is a really nice package btw) but is definitely
copyrighted. However the licensing on these doesn't really encourage code
reuse rather just personal code modification, and it would seem to me
that code reuse might be beneficial in some circumstances rather than
everyone reimplementing everyone elses algorithms/methods/force fields.

	In any case i'm curious as to what is out there already if
anything.

end-message----------------------------------------------------------------

Summary ::

The programs below all have source, i've put the GPL'd code and GPLLike
code at the top . I did some culling from the meta pages and put in some
brief  descriptions. As is hopefully obvious, don't trust me or my
descriptions but take a look at the pages (links provided) for the real
details. Hopefully this list will be useful to anyone who'd like
to join incorporated their code into a GPL'd program and/or
use algorithms from a gpl'd project.

Apologies for all ytpos and any/all misrepresentations etc.. -Avi.

Set (1) GPL'd Code.

    AMMP GPL MD Code (Apparantly has DFT incorporated!)

         http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

    MOLDY  GPL'd rigid body md

         http://www.earth.ox.ac.uk/~keith/moldy.html

    MOSCITO :: MD Code. ||ized. OPLS/AMBER/Gromacs. GPL'd

       http://ganter.chemie.uni-dortmund.de/~pas/moscito_info.html

    MMTK  Open Sourced python based molecular modelling tool kit

          http://starship.python.net/crew/hinsen/MMTK/

    Ghemical GPL Molecular modelling package

       http://www.uku.fi/~thassine/ghemical/

    EGO_VIII  || MD Code (GPL).

       http://www.lrz-muenchen.de/~heller/ego/egointro.html

    NAB :: Nucleic Acid Builder (implements amber95 :: has
           Generalized Born) (GPL)

        http://www.scripps.edu/case

    MPQC :: Massively Parallel Quantum Chemistry program. GPL'd.

        http://aros.ca.sandia.gov/~cljanss/mpqc/

    ORAC MD for solvated biomolecules. GPL'd.

       http://www.chim.unifi.it:8080/orac/

Set two :: (soon to be) GPLish?? Allows redistribution??

    CHIMP :: "generic tool for modelling of chemical phenomena."
             GPL'd. but "unavailable" ??

    http://chimp.sourceforge.net/

    GROMACS : || MD code . Being considered for GPL

         http://md.chem.rug.nl/~gmx

    NAMD :: || MD Code. "Licensee may redistribute without restriction works with
                         up to 1/2 of their  non-comment source code derived
                         from at most 1/10 of the non-comment source
                         code developed by Illinois and contained in the
                         Software, provided that the above directions for notice
                         and acknowledgement are observed." (see below)

    http://www.ks.uiuc.edu/Research/namd/

    Cornell's Computational Biology TOOLS (Lots of free MD
     etc packages from R. Elber and H. Scheraga) :: Free for all
     use, as long as you don't sell it to people for $$.

      http://www.tc.cornell.edu/CBIO/

    NWCHEM  Massively || QM/MM code (free as long as you aren't a U.S.
            "baddy" )

      http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html

    B :: Java based MD Code (Less restrictive than GPL)

       http://www.scripps.edu/~nwhite/Biomer/index.html

Set (3) Other. Many here are "Free for Academic use" which  generally
    means no redistribution (Free use; no abuse :)), but as always look at
    the pages.  Incidentally, free for academic use is nice but *imho* GPL
    (and friends or  at least allowing redistribution)     is nicer as it
    means i (and my friends)  can try out your algorithm/force
    field/minimizer/integrator/solvation model  etc etc w/ my (insert
    previous list in reverse order)  and let others try it
    w/out having to reimplement each spoke on this wheel, which  as far
    as I can gather pretty much everyone is doing.

    Tinker :: (Copyright WUSTL/Tinker but see below w/ regards
              using/redistributing source)

              http://dasher.wustl.edu/tinker/

    DYNAMO :: F90 modules for QM/MM (OPLS-AA) free of charge.
             No redistribution.

      http://www.ibs.fr/ext/labos/LDM/projet6/welcome_fr.htm

    LAMMPS :: || MD code. Free for academic use. No redistribution.

      http://www.cs.sandia.gov/~sjplimp/lammps.html

     GULP :: simulation of periodic solids/clusters.. :: free for
            academics. no redist.

       http://www.ch.ic.ac.uk/gale/Research/gulp.html

     DL_POLY || MD code :: Free for Academic Scientists pursing
        non-commercial science.

        http://www.dl.ac.uk/TCSC/Software/DL_POLY/main.html

     ARTWork :: MD/MC code based on "Effective Medium Theory" , avail. for
        acad. purposes  "as is"

        http://www.fysik.dtu.dk/~stoltze/artwork/artwork.html

     Autodock :: Docking code, free for academic use.

       http://www.scripps.edu/pub/olson-web/doc/autodock/

    MDYNAMIX :: source code available (couldn't find license on web page)

      http://www.fos.su.se/physical/sasha/md_prog.html