[Jmol-developers] Difficulties with Gaussian

[Miguel <mi...@jm...>]

I have uncovered a problem when dealing with Gaussian files.

Detail
------
Rene has been helping/encouraging work on Gaussian files (and all the
other 'computational' packages like Gaussian). One of the changes he did
was retain all the intermediate steps during optimizations.

That is a good thing.

Now, the file samples/gaussian/H2O_NoSymm.out does not contain a 'Standar=
d
orientation:' ... it only contains an 'Input orientation:'

In the spirit of the work that Rene has done I thought that I would also
store the 'Input orientation:' so that it could be displayed in Jmol. Tha=
t
was easily done.

However, it uncovered a problem ... a problem that has not raised its ugl=
y
head in a long time.

The 'center of gravity' of the molecules is calculated across all of the
models/frames. This is then used as the center of rotation for all models=
.

You cannot calculate the cg of each frame independently because:
 - in multi-frame animations the atoms are moving ... therefore the cg of=

each frame is different ... therefore the center of the frames is not
stable ... therefore you must calculate the cg of the frame set as a
whole

 - in multi-model .pdb files with more than one conformation you want the=

majority of the atoms to line up ... that way you can switch from one
conformation to another and see the areas that are different ...
therefore all the frames must have the same cg cartesian point.

The problem is that this approach does not work well when the Input
orientation: is included with the Gaussian set. This is because the Input=

orientation: can be off-centered. So the center-of-gravity of the Input
orientation: messes up all the other models.

For the present time I am going to leave this code in ... so that you
eager Gaussian users can take a look at it.

In the short term we can just 'sweep this problem under the rug' by
removing support for the 'Input orientation:' ... but in the longer term
we are going to have to come up with some solution.


Miguel