That's probably because I don't have any IRC output from GAMESS. If you
send one to [email protected], I can fix that.
On Tue, Aug 20, 2013 at 7:13 AM, Whitwell, George <[email protected]>wrote:
> 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]>wrote:
>
>>
>>
>>
>> On Mon, Aug 19, 2013 at 9:37 PM, Whitwell, George <[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]]
>>> *Sent:* Monday, August 19, 2013 6:12 PM
>>> *To:* [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]>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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Introducing Performance Central, a new site from SourceForge and
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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
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Introducing Performance Central, a new site from SourceForge and
>>> AppDynamics. Performance Central is your source for news, insights,
>>> analysis and resources for efficient Application Performance Management.
>>> Visit us today!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>>> _______________________________________________
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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
>
>
>
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
> Visit us today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central is your source for news, insights,
analysis and resources for efficient Application Performance Management.
Visit us today!
http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
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