Thanks, Bob.
REVERSEMODELS works as advertised. I have to load the first file reversed -
they both start at the saddle point.
I tried getproperty modelinfo.models.energy to retrieve the energies. I get
back "" for all my 57 frames, so I think that these values may not be extracted
from the GAMESS output.
I can picture how to write a series of molecular files from the two models.
I'm wondering if there is a preferred approach to writing out one file with all
of the frames in sequence - like a Biosym .car or MSI .trj
George
________________________________
From: Robert Hanson [hans...@stolaf.edu]
Sent: Monday, August 19, 2013 6:12 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] reordering IRC frames and pasting two halves together
For the second one, use:
load append xxxx.gamess filter "REVERSEMODELS"
has worked in the past for me, at least for Spartan files. After that, you
might have to delete one or more models.
You also may need to do some alignment. For that see
http://chemapps.stolaf.edu/jmol/docs/index.htm?search=frame%20align&ver=13.3.4_dev_2013.08.19
On Mon, Aug 19, 2013 at 3:22 PM, Whitwell, George
<gwhitw...@ncwc.edu<mailto:gwhitw...@ncwc.edu>> wrote:
Hi,
I have GAMESS output from both sides of the reaction coordinates from a
Cl-CH3-Br anion intermediate as an example of an SN2 reaction. I can load both
output files in Jmol as different models and animate them consecutively;
however, since they both run downhill, it isn't really the sequence of the
desired SN2 trajectory.
How can I reverse the order of the frames of one model and is there a preferred
way to save the collection of frames from both models in one file? Also, is
Jmol reading the energy of each structure and can I access that as a variable?
Thanks for any help,
George
Dr. George E. Whitwell
Associate Professor - Chemistry
North Carolina Wesleyan College
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Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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