LLM path analysis

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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.