On Mon, Aug 19, 2013 at 9:37 PM, Whitwell, George <gwhitw...@ncwc.edu>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 [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>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
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