Subject: CCL:GPL'd MD packages :: Summary

From: Avijit Ghosh <[email-masked]>
Date: Tue, 6 Feb 2001 20:22:10 -0500 (EST)

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)
          (Free to do anything one would do w/ GPL :: see below)

        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

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

    B :: Java based MD Code (couldn't find license on home page)

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

------------------------------------------------------------------
Original responses ::
------------------------------------------------------------------
> From [email-masked] Tue Feb  6 18:24:23 2001
Date: Thu, 1 Feb 2001 13:29:28 +0100 (CET)
From: David van der Spoel <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

On Wed, 31 Jan 2001, Avijit Ghosh wrote:

>
>	I was wondering whether anyone has any GPL'd code for MD?
We are considering licensing GROMACS http://md.chem.rug.nl/~gmx under GPL.
Right now we have a handful of developers using CVS. The code is
definitely free (as in beer) for academics. One source of worry is the
qulaity control. Obviously the results should be correct, and that means
someone has to keep control over the source code. A linux kernel like
model could be used for that. GROMACS is not (yet) very good in different
forcefield (for proteins it is only GROMOS87 and GROMOS96, for small
molecules one can write a topology manually or
semi-automatically). However the code is *much* faster than anything else,
and much easier to use due to our script-free (tm) user interface.
So if you are interested in contributing force field wrappers to GROMACS
you are more than welcome.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

> From [email-masked] Tue Feb  6 18:24:29 2001
Date: Thu, 1 Feb 2001 08:11:17 -0600 (CST)
From: Frederick P. Arnold Jr. <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

Hello,

Moldy, from Keith Refeson at Oxford is GPL'd.  It's a rigid-body,
pair-potential based package, so it's not what you're looking for for
biomolecules (probably), but you're certainly free to add whatever is
missing.  http://www.earth.ox.ac.uk/~keith/moldy.html

you should probably also look at MMTK (Konrad Hinsen), which is a
biomolecule forcefield. http://starship.python.net/crew/hinsen/MMTK/

There is, of course, the Ghemical project.  Pretty raw at the moment, but
with a nice minimalist builder and force-field. GPL'd, and we'd love to
see some extra participation on making it a usable package.  (my only
contribution, regrettably, was rounding up a volunteer graduate student,
and securing funding for an undergraduate programmer from Northwestern.
Maybe someday I can start writing code again.)
http://www.uku.fi/~thassine/ghemical/

Finally Tinker, while definitely copyrighted, is not onerously licensed
(no worse than GAMESS-US).  You know this, but maybe you should discuss
wtih Jay Ponder what you want to use the code for.  Similarly licensed,
but higher-performance (if you have the hardware lying around), is NW-Chem
> from PNL.  (http://www.emsl.pnl.gov:2080)  Designed for massively-parallel
execution, and written in a mutant dialect of Fortran, it's still a pretty
complete package, and not onerously licensed.

						-Fred

					Frederick P. Arnold, Jr.
					NUIT, Northwestern U.
					[email-masked]

> From [email-masked] Tue Feb  6 18:24:41 2001
Date: Thu, 1 Feb 2001 15:13:36 +0100 (MET)
From: Denys Bashtovyy <[email-masked]>
To: [email-masked]
Subject: GPL'd MD packages

Hi  Avijit,

please, have a look at these:
1)AMMP
http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html
2)EGO_VIII
http://www.lrz-muenchen.de/~heller/ego/egointro.html
3)Ghemical
http://www.uku.fi/~thassine/ghemical/
4)MMTK (is it under GPL?)
http://dirac.cnrs-orleans.fr/programs/MMTK/index.html
5)Moldy
http://www.earth.ox.ac.uk/~keith/moldy.html

Best wishes,

-- 
Denys Bashtovyy
[email-masked]
http://www.brc.hu/biophysics/memstruc.htm

Sent through GMX FreeMail - http://www.gmx.net

> From [email-masked] Tue Feb  6 18:24:44 2001
Date: Thu, 1 Feb 2001 09:29:03 -0600 (CST)
From: Geoff Hutchison <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

> 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.

I am quite interested to hear if you get any responses. IMHO, it would be
wonderful if more code was available under the GPL, which I personally
think is quite useful for academic work. (For example, people could sell
the code, but you could still get the source to see what's new.)

Of course I'm a bit biased. I'm helping with the OELib/Babel 2.0 project,
which is under GPL and the Ghemical molecular editor, which is also
GPL'ed.

The Ghemical source has a Tripos-like force field, but it's hardly a full
implementation.

--
-Geoff Hutchison		<[email-masked]>
Ratner Group			(847) 491-3295
Northwestern Chemistry		http://www.chem.northwestern.edu/

> From [email-masked] Tue Feb  6 18:24:46 2001
Date: Thu, 01 Feb 2001 09:42:47 -0600
From: Jay Ponder <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

Dear Avijit Ghosh,

     I saw your email to the CCL. Thanks for the mention of the
TINKER package.

     I certainly want the TINKER code to be widely used, and I'm
happy to have others modify the code for their own use. The problem
with making the code "public domain" is at least two-fold. First,
is the fact that for my own selfish purposes I want to have control
of the future of the package. I've put many years of effort into
getting the code to its current point, and if someone with greater
bandwidth to the comp. chem. community came in and effectively took
it over, I would be upset. Second, and less personal, it is very,
very easy to break a code as complex as TINKER. We support multiple
force fields and use some rather fancy algorithms for some things.
I get submissions of code from other people all the time as possible
additions to TINKER, and you would be amazed at the number of these
that are fine for what they intend, but break some other aspect of
the package. If TINKER were truly public domain, with lots of people
hacking for their own purposes, I fear that it would quickly become
a mass of incompatible and partially broken code. To the extent that
TINKER is useful, it's because I and the folks in my very small
group know every line of code and all the inevitable dependencies.

     The above said, I have allowed three groups to use TINKER in
packages they redistribute: (1) TINKER is the force field engine
in the GAMESS QM/MM implementation, (2) TINKER is the engine for
the TINKERATE rate calculation package from Truhlar's group at
the Univ. of Minnesota, and (3) TINKER's force field implementation,
GB/SA solvation model and dynamics code is used with essentially
no modification in Pande's Folding@Home distributed dynamics
project at Stanford. I allowed these uses because I knew or knew
of the people involved and I was fairly sure they would not break
things, or allow their use of TINKER to get out of hand. (In that
regard, I now sort of regret the Folding@Home use, since lots of
Pande's users are non-chemist CS types who are horrified at the
thought that Fortran code is running on their machines, want to
rewrite the whole thing in C++, and generally have very little
idea what they are getting into....).

     If you have some specific desired use for the TINKER code,
please send me some email explaining. If, on the other hand, you
simply think it would be "nice" if their were a GPL'd dynamics
package, I would reply that I'm not sure the world is ready to
deal with that yet--the science behind the codes is not yet mature
enough to be ossified into generic public domain packages.

                        Best wishes, Jay P.

-- 
Jay W. Ponder                          Phone:  (314) 362-4195
Biochemistry, Box 8231                 Fax:    (314) 362-7183
Washington University Medical School
660 South Euclid Avenue                Email:  [email-masked]
St. Louis, Missouri 63110  USA         WWW:    http://dasher.wustl.edu/

> From [email-masked] Tue Feb  6 18:25:16 2001
Date: Thu, 1 Feb 2001 10:23:19 -0800
From: David Case <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Cc: [email-masked]
Subject: Re: CCL:GPL'd MD packages

On Wed, Jan 31, 2001, Avijit Ghosh wrote:
>
> 	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* ).

NAB (Nucleic acid builder) implements the Amber95 force field.  It includes
generalized Born calculations, but *not* periodic boundary conditions
simulations, so it may or may not satisfy particular needs.  In spite of the
name, it is designed to work on proteins as well as nucleic acids.

Whether or not the code itself (mainly in file sff.c) would be useful
to transfer to other applications is of course a subjective decision, but
you are certainly free to do anything allowed by the terms of GPL.

See my web page (below) for more info.

....good luck...dac

-- 

==================================================================
David A. Case                     |  e-mail:      [email-masked]
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================

> From [email-masked] Tue Feb  6 18:25:31 2001
Date: Thu, 1 Feb 2001 18:04:08 -0500 (EST)
From: Cezary Czaplewski <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

You can look at http://sal.kachinatech.com/Z/2/index.shtml

Some of MD programs listed there are released under GPL but I have never
tryied personally any of them.

			czarek

> From [email-masked] Tue Feb  6 18:25:48 2001
Date: Mon, 5 Feb 2001 09:45:49 +0000
From: Keith Refson <[email-masked]>
Subject: CCL:GPL'd MD packages
Resent-Date: Mon, 5 Feb 2001 09:47:25 GMT
Resent-From: Keith Refson <[email-masked]>
Resent-To: Computational Chemistry List CCL <[email-masked]>

You will find links several MD packages on

http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html

However only a few are GPLed. I would have expected that the GPL be
adopted more widely in science than it has been, since it is pretty
much an expression of the purest ideals of freely sharing knowledge.
However it seems that the constant pressure for cash is stifling these
ideals.

Keith Refson

-- 
Dr Keith Refson,        "Paradigm is a word too often used by those who would
Dept of Earth Sciences      like to have a new idea but cannot think of one."
Parks Road,                  -- Mervyn King, Deputy Governor, Bank of England
Oxford OX1 3PR, UK
Keith.Refson@                       Tel: 01865 272026
             earth.ox.ac.uk         Fax: 01865 272072

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> From [email-masked] Tue Feb  6 19:54:40 2001
Date: Thu, 1 Feb 2001 10:03:32 -0600 (CST)
From: Jim Phillips <[email-masked]>
To: Avijit Ghosh <[email-masked]>
Subject: Re: CCL:GPL'd MD packages

Hi,

Depending on your definition of reuse, you may find this clause in the
NAMD/VMD licenses relevant (read the whole license, though):

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.  Any other
                   distribution of the Software or any derivative work
requires a separate
                   license with Illinois.  Licensee may contact Illinois
([email-masked]) to
                   negotiate an appropriate license for such distribution.

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

-Jim

On Wed, 31 Jan 2001, Avijit Ghosh wrote:

>
> 	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.
>
> 	-Avi
>
> (W/ apologies about fomenting the Fortran/C++ war into a source
>  code licensing war :) )
>
> Actually w/ regards to programming languages, let me mention that I did
> my undergrad. in CS and at the time we did every class (except for
> operating systems) in Pascal which isn't obviously "useful". Really,
> language doesn't matter; you can write equally crap/unmaintainable code
> in all! :)
>
>
>
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