CCL:G: Gaussian G09- Relaxed scans in Cartesian coordinates

 Sent to CCL by: Cory Pye [cpye##ap.smu.ca]
 Jason,
 It should be possible to use opt=z-matrix to do your relaxed PES scan for the
 coordinates that you want to vary. For the atoms that move around a lot, you
 can use cartesians as part of the z-matrix, if needed, to avoid problems with
 angles becoming 0 or 180. An example might be to use a z-matrix to represent
 your solute and cartesians to represent the solvating water molecules.
 -Cory
 On Wed, 9 Oct 2013, Jason Boettger jdb488=psu.edu wrote:
 >
 > Sent to CCL by: "Jason  Boettger" [jdb488!^!psu.edu]
 > Hi folks!
 >
 > This is a humble request for some assistance on a relaxed PES scan in
 > Gaussian G09 (rev. c01 for what it's worth). I am trying to perform a
 relaxed
 > PES scan to determine the activation energy of an aqueous reaction, which I
 > am simulating with several water molecules. When I set up a typical relaxed
 > PES scan using ModRedundant commands, my model runs typically crash after a
 > few optimization steps (not even scan steps, just the constrained
 > optimization steps). I believe the shifting of water molecules in my model
 > causes the automatically-generated redundant internal coordinate system to
 > break, and I get errors of the form "Eigenvalue # is ### should be
 less than
 > 0.000 Eigenvector...Error in redundant internal coordinate system." I
 believe
 > these errors would be fixed if I could manage to do the scan in Cartesian
 > coordinates, but ModRedundant commands don't work in Cartesian coordinates.
 > This is all very frustrating because it forces me to continually re-submit
 > these jobs, wasting precious time in computing queues.
 >
 > Well, that is the nature of my problem. Here are some potential solutions I
 > have come up with, but I need your help in how to implement them, and in
 > knowing if they are even possible:
 >
 > First, I could use a sequence of optimization jobs that I string together
 > with Link1. I could enter the Cartesian coordinates of all atoms, then
 freeze
 > the two atoms of interest I want to scan (1), then perform a constrained
 > optimization in Cartesian coordinates. Then, I could use Link1, recover the
 > newly optimized geometry with geom=check guess=read, and then somehow (2)
 > modify the Cartesian coordinates of the two atoms of interest so that they
 > are closer by, say, 0.1A. Alternatively, I could convert back to redundant
 > internal coordinates after each constrained optimization step and do a one-
 > step rigid PES scan to increment the two atoms of interest together, then
 use
 > Link1 to switch back to a constrained optimization in Cartesian coordinates
 > (3). These proposed solutions would result in very long input files, but
 > creating them by means of a Python script should be fairly straightforward.
 > My questions are thus: (1) How do you freeze atoms in Cartesian
 coordinates?
 > It is easy to do in redundant internal coordinates, but I couldn't get any
 of
 > the old solutions posted to the CCL list for G03 and earlier to work for
 me.
 > A quick example would be VERY helpful. (2) Is there a way to modify
 Cartesian
 > coordinates that I have recovered with geom=check guess=read? Again, an
 > example would be very helpful. (3) Are there any problems in switching back
 > and forth between coordinate systems that might arise using this method?
 I'd
 > still need to figure out how to freeze the two atoms of interest.
 >
 > Second, I could attempt to work in redundant internal coordinates, but
 > manually choose those coordinates which I want to use to describe my
 system.
 > (1) How can I go about constructing these; can anybody point me to a
 > tutorial? (2) Also, is there a way looking at the error output which lists
 > the eigenvectors to tell which redundant internal coordinates are causing
 my
 > issues?
 >
 > Third, there could be some magic way to actually do relaxed PES scans in
 > Cartesian coordinates. Does anybody know a way? The online GAUSSIAN manual
 is
 > heinously unhelpful at times.
 >
 > Thank you so much for making it to the bottom of my long message, and
 again,
 > any help would be appreciated- figuring out how to freeze Cartesian
 > coordinates would be a big step in the right direction! And let me know if
 it
 > would help for me to clarify anything. Thanks in advance!
 >
 > Jason Boettger
 > PhD Student, Geosciences, Penn State University
 > jdb488,psu.edu>
 >
    *************    !  Dr. Cory C. Pye
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