[Molecularmechanics] first steps

[David van der Spoel]

On Tue, 2003-10-21 at 10:00, Peter Murray-Rust wrote:
> <Michael Shirts>

> 
> At a recent meeting CECAM meeting, sponsored by the FSatom project
> (http://www.fsatom.org) a working group was formed to try
> to develop open standards in the field of biomolecular computing.
> Currently the molecular mechanics developers that have agreed to work
> together for open standards represent CHARMM, AMBER, GROMACS, and
> TINKER.  We hope that as many code base developers as possible will be
> able to join the effort.
> 
> I think these are an excellent start. I developed a proof-of-concept for 
> adding XML to TINKER code for i/o and will be happy to resurrect it.  This 
> was initially F77 statements in code, but would now include  XML/F90 i/o 
> libraries. Are we agreed that F90 is taken as a universally available 
> technology?
NOOOOOOOOOO!!!!!!!!

We definitely do not want to use fortran. If anything in this work group
is to go beyond the definition (i.e. file format description) phase, we
should use common libraries like libxml2 that come bundled with the OS,
and base I/O routineson that. It shouldn't be hard to come up with a
fortran frontend for such routines. 

The problem is to link C code (that does I/O) with code that does I/O in
fortran. This will severely affect the portability of the code. The
other way around is much easier.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel@xray.bmc.uu.se	spoel@gromacs.org   http://xray.bmc.uu.se/~spoel
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