[gmx-developers] DCD / Licence

[Axel Kohlmeyer]

On Fri, 2009-07-03 at 12:58 -0400, Roland Schulz wrote:
> Hi,
> 
> I am using the VMD DCD reader. 

that is what i thought.

> Using the VMD plugin API would add 3 addiotional source files (hash.c,
> molfile_plugin.h, vmdplugin.h).

> Does this matter? Should I do this so that we can easily add further
> vmd supported types in the future?

if you use the molfile API, you automatically add _all_ formats
that the molfile plugins support. that would include for example
native formats of LAMMPS, desmond, amber, amber/netcdf on top
of .dcd without any extra coding effort from you. 

i'm not sure why you'd need hash.c. for writing an interface to
the plugin API you should only need files from the include directory.
i'd suggest you start from the latest (cvs) code, as VMD-1.8.7 is about
to be released very, very soon and that would require vmdplugin.h,
molfile_plugin.h and vmdconio.h.

there have been some significant improvements. for example, the improved
plugin API has support for reading angle, dihedral, improper
definitions, or velocities (for file formats that support it). 

the main advantage is that you don't have to maintain the .dcd
(or others format) readers yourself and keep it in sync with 
the VMD/molfile code base. there is already too much code 
replication already. for VMD i'm planning to adjust the gromacs
support to use libxdrfile from the gromacs distribution, for example.

cheers,
   axel.


> Roland
> 
> On Fri, Jul 3, 2009 at 11:59 AM, Axel Kohlmeyer
> <akohlmey at cmm.chem.upenn.edu> wrote:
>         roland,
>         
>         On Fri, Jul 3, 2009 at 6:44 AM, Roland Schulz<roland at utk.edu>
>         wrote:
>         > Hi,
>         >
>         > what do you think about adding DCD read support to the
>         tools? Quite a few
>         > people in our group use the tools but (for a number of
>         reasons) do the
>         > simulation still with other MD packages. It is inconvenient
>         to have to
>         > convert the trajectories.
>         
>         
>         instead of adopting code to only read .dcd files,
>         why don't you write an interface to the VMD molfile API?
>         should be even less work and then you would interface
>         gromacs to a large number of file formats. also it would
>         avoid replicating and code (and problems with diverging
>         developments and missing bugfixes) and also you can add
>         new file formats or updated readers/writers
>         on the fly through the dynamic loading of plugins.
>         
>         cheers,
>          axel.
>         
>         p.s.: we're also in the process of gradually revising the
>         molfile API to make it more flexible and powerful and
>         particularly add support for "out-of-core" processing of
>         a collection of files (primarily for VMD but not limited to
>         it).
>         that might be interesting for gromacs tools just as well.
>         
>         
>         >
>         > Is it OK to add code which is under the University of
>         Illinois Open Source
>         > License? It is GPL compatible so does not cause license
>         conflicts
>         >
>         (http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License).
>         >
>         > Roland
>         >
>         > --
>         > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>         > 865-241-1537, ORNL PO BOX 2008 MS6309
>         >
>         
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>         --
>         
>         =======================================================================
>         Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu
>         http://www.cmm.upenn.edu
>          Center for Molecular Modeling   --   University of
>         Pennsylvania
>         Department of Chemistry, 231 S.34th Street, Philadelphia, PA
>         19104-6323
>         tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel:
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>         better idiot.
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> 
> 
> -- 
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
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-- 
=======================================================================
Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.