## Linear Least Motion path analysis

MacMolPlt has the ability to automate the generation of a Linear
Least Motion (LLM) path connecting two know structures. This path can
be constructed in either cartesian coordinates or in Z-matrix style
internal coordinates. LLM paths can be useful for locating a
transition state, or at the very least, putting an upper bound on the
height of a transition state. One problem with an LLM path using
cartesian coordinates is that bonds may be overly stretched or
compressed causing large variations in the energy. To avoid this
problem you can use internal coordinates for the LLM path. Creating
an LLM path in MacMolPlt is quite easy.

- First you need a window with the two endpoints of the LLM in
adjacent Frames. One way to accomplish this is:
- Create a new document.
- Paste in the coordinates of the starting point.
- Append a new empty frame using the Append New Frame menu
item
- Paste the coordinates of the endpoint into the empty frame.

- Next minimize the differences between frames by positioning
the Frames sequence to the first structure and choosing the
Minimize Frame Movements. This will zero out any translation or
rotations between the two structures.
- If you wish to use internal coordinates then you must specify
a valid set of internal coordinates in the Coordinates Window at
this time (Open the
Coordinates window,
choose Internals and modify the default list as needed).
- Next choose the Create LLM Path... menu item.
- Enter the number of LLM path points to create (the total
number of points on the path is 2 plus the number you enter
here).
- If you wish to use internal coordinates check the box.
- Hit Create LLM.

That's it. You will now find the requested number of structures in
between the two structure you input. I recommend saving the LLM path
at this point. You probably already have the energies for the two
endpoints. However, you still need them for the points MacMolPlt
created. To obtain these energies you will need to generate a series
of input files to run single point energy calculations. You can
generate these files by hand (by copying the coordinates of each
frame out of MacMolPlt) or use MacMolPlt's
Input Builder window to
generate the input files for you (still one file at a time though).
Once the calculations are done you can copy the desired energy
information and use the Set Frame Energy... menu item to set the
energy of each geometry. Once all points are input you can view the
energy graph to see how
the LLM path behaves.