It now reads the energy of the first model, but only the positions for the rest.
Readers of this conversation should note the typo in the getProperty below:
should be-> print getProperty("modelInfo.models[1].energy")
________________________________
From: Robert Hanson [[email protected]]
Sent: Tuesday, August 20, 2013 12:24 AM
To: [email protected]
Subject: Re: [Jmol-users] reordering IRC frames and pasting two halves together
Gaussian missing energy -- that should be fixed for
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.19b.zip (uploading
now). Please let me know if it is not.
should be
print getProperty("modeInfo.models[1].energy")
for example, or from JavaScript:
var e = Jmol.evaluate(jmolApplet0, 'getProperty("modeInfo.models[1].energy")')
On Mon, Aug 19, 2013 at 10:30 PM, Robert Hanson
<[email protected]<mailto:[email protected]>> wrote:
On Mon, Aug 19, 2013 at 9:37 PM, Whitwell, George
<[email protected]<mailto:[email protected]>> wrote:
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 fix that.
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
select *
write COORDS xxx.sdf
COORDS and SDF are important. That tells Jmol to keep the models separate.
George
________________________________
From: Robert Hanson [[email protected]<mailto:[email protected]>]
Sent: Monday, August 19, 2013 6:12 PM
To: [email protected]<mailto:[email protected]>
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
<[email protected]<mailto:[email protected]>> 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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--
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
--
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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AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
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