Nick,
This cyclohexane file is ours (http://www.cmbi.ru.nl/mol4d) , and we use the second line of the xyz file (a line free for comment) to pass on information from one application to the next.
I am trying to understand the m-xyz file format and methods for creating them for animations.
Please can someone explain the origin of the "FOR REACTION COORDINATE" data item in this sample m-xyz file?
Does Jmol make any use of this data?
cyclohexane_movie.xyz from http://jmol.sourceforge.net/demo/animation/
18
HEAT OF FORMATION = -38.59443 KCAL = -161.47910 KJ; FOR REACTION COORDINATE = -176.55290 DEG
C 0.0000 0.0000 0.0000
C 1.5158 0.0000 0.0000
C 2.0591 1.4144 0.0000
C 1.5171 2.2065 1.1728
C 0.0013 2.2193 1.1610
C -0.5553 0.8094 1.1544
snip
The computational script abstracts the energy and reaction coordinate for each point of the animation from the (mopac etc) output, and writes it into the second line of each coordinates block.
This m-xyz file is read by the next script that creates a web page with the Jmol animation and, from the data on the second line, a clickable plot of energy vs reaction coordinate (or whatever coordinate you scan in the computation). Jmol is not supposed to do anything with it (yet).
Hens Borkent CMBI, Radboud University Nijmegen
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