[Molecularmechanics] first steps

[Jakob Schiotz]

 > I completely agree. One of the biggest problems to interoperability is the 
 > implicit semantics in many programs. By externalising the semantics you get 
 > a much cleaner design as well as a better understanding of what the program 
 > is actually doing. I'm fairly confident that for most systems the XML can 
 > abstract the force field. As a general rule, when something proves 
 > difficult in XML it tells you there is a fundamental design feature that 
 > must be addressed.

I am afraid that few programs, if any, will read the force field
description from the XML file, and then use it.  Rather, it will have
the force field implemented in C/C++/Fortran/Whatever.  The XML force
field will at most be recognized.  So in most cases, the XML force
field only documents the "real" force field.  This is still useful,
but we will quickly come in situations where the XML definition
differs from the actual implementation.  If the XML definition is never
used for real calculations, it will essentially be "untested code",
and therefore buggy.  

Perhaps it will be just as useful to represent the force field by a
single string which identifies it.  Or two strings, one with a name
and another with one or more journal references.

Jakob

-- 
Jakob Schiotz, Ph.D.             !  Email: schiotz@fysik.dtu.dk
CAMP, Department of Physics      !  WWW: http://www.fysik.dtu.dk/~schiotz/
Technical University of Denmark  !  Phone: (+45) 45 25 32 28
DK-2800 Lyngby, Denmark          !  Fax:   (+45) 45 93 23 99