Subject: Re: CCL:OFF Files and MD

From: [email-masked] (Konrad HINSEN)
Date: Mon, 18 Mar 1996 15:32:17 -0500

> Before I start worrying about OFF at all, I would really like to know:
> 
> 	1) When will there actually be a MD-program that understands OFF?
> 	2) Will OFF only be supported by AMBER (and SPASMS) or is there a
> 	   chance that other MD-programs (CHARMM, discover) will read OFF.
> 	3) Is there a (definitive) specification of OFF somewhere.
> 	4) Is there any other movement towards a universal file-format for
> 	   the specification of chemical systems for MD-simulations?

Why just MD simulations? I'd love to see a general file format for
*all* computational chemistry applications. Wouldn't it be nice
to be able to tell your ab-initio code to calculate the energy
for the 42nd configuration of an MD trajectory?

There is of course the small problem that various programs need
various information, and that you can never know in advance what
information other programs might possibly need. Therefore a general
file format would have to be extensible: each file would consist of
sections starting with identifying tags, and every program would
ignore tags it doesn't need or understand (those who happen to know
TIFF will know what I am talking about...). There would be standard
tags and program-specific tags. Such a file format can be extended
arbitrarily without giving up compatibility with old programs.  I've
used this approach a long time ago in a word processing program and in
spite of many updates the first version can still read the files
written by the latest.

Another important feature is to have both a text and a binary
version of the format, plus a simple program to convert between
the two.

Probably something like this can be implemented on top of
existing standards/libraries like netCDF. But defining a really
good format will take a lot of work, so I suppose it won't
happen any time soon :-(

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From: [email-masked] (Peter Shenkin)
Date: Mon, 18 Mar 96 18:22:08 -0500

> From [email-masked]  Mon Mar 18 17:26:40 1996

> *all* computational chemistry applications. ...

Stay tuned for CEX (Chemical EXchange).  This is being assembled
quietly by a small consortium, and we want to get some sample
applications out to polish the implementation before announcing
it to the world.  

The impetus behind it is Frank Brown at Glaxo;  Dave Weininger
of Daylight Software has put together an underlying language
for passing data, and a few programs (RasMol, DGEOM) know how
to "speak" it already.  I'm beginning a MacroModel port.  

It's not so much a file format as a chemical database API.  Using
the API, one can write into a file or read from a file, or 
read/write to/from any CEX stream (which might be a program, for 
example).

Hopefully, sample implementations will be available within a
few months.  In the meantime, see:

	http://www.daylight.com/emug/cex-talk-dw/cex-talk.html

-P.
**************** In Memoriam, Minnie Pearl, 1913-1996, RIP *****************
*** Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ., ***
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