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
>>>
>>>
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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
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analysis and resources for efficient Application Performance Management.
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