I've added show minimization to the next upload of the documentation.
Thanks.
You have to remember that this is a huge set of parameters that were
optimized for a specific data set. I would refer you to the literature
reference. Mostly you cannot get anything significant from any one
parameter, and deficiencies in one might result in overcompensation by
others. There's only so much one can do to optimize something like this. Of
course, the only number that matters is the total energy. It's what you get
for your money!
Bob
On Mon, Feb 24, 2014 at 10:00 AM, James <ja...@ryley.com> wrote:
> Thanks Robert, I figured it must be available somehow - almost everything
> is :) I would mention thought that "show minimization" isn't in the docs
> as far as I see at
> http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=14.2#show. Good
> thing to add, unless I just missed it!
>
> That leaves me with 2 questions:
>
> 1) Is the easiest thing to do to get this data into arrays just to parse
> the output of "show minimization", or are these already stored in some more
> convenient format?
>
> 2) This might be just my admittedly inaccurate assumption, at least in
> some cases, that molecular mechanics models have an intuitive "real world"
> representation (meaning, e.g., the stretch term truly equates to stretch,
> and the bend term truly equates to bend, etc.), but the mmff94 results (and
> I've seen this with mm+ in HyperChem also) don't seem to break down as I
> would think. For example, cyclopropane has a lot of ring strain (estimated
> at 27.6 kcal/mol in the literature), the majority of which comes from angle
> strain, not torsional strain (~9 kcal/mol).
>
> mm+ VASTLY underestimates both total strain and angle strain. mmff94
> substantially overestimates torsional strain while again vastly
> underestimating angle strain (mmff94 actually overestimates total strain,
> storing a lot of it in an "electrostatic" category. Note that the lack of
> agnel bending strain energy seems to come from the fact that both of the
> force fields seem to be using a reference angle of 60 degrees for
> tetrahedral carbon, which is actually ideally 109.5 degrees. I know in the
> case of mm+ this is on purpose -- 3 and 4 membered carbon rings get
> assigned special reference values, so I assume the same thing is happening
> in mmff94.
>
> Which brings me to the question: Do these energy numbers, and the
> breakdown of the energies into the various categories, really mean
> anything? Or should I just think of them as being abstract equations that
> are used to curve fit the molecular mechanics energy minimization to
> empirical data? Or, do they actually work fairly well in most cases and
> I've just picked some weird edge cases where the parallelism of the
> formulas and the real world break down?
>
> I know #2 isn't really a Jmol topic, but rather computational chemistry in
> general. If you'd prefer, and anyone is interested in discussing this off
> list, I'd really like to talk to someone who has more experience with this
> than I.
>
> Sincerely,
> James Ryley, PhD, Patent Agent
> SumoBrain: Intellectual Property Solutions & Data
> AcclaimIP <https://www.acclaimip.com/> |
> FreePatentsOnline.com<http://www.freepatentsonline.com/>|
> SumoBrain.com <http://www.sumobrain.com/> |
> BioMedSearch.com<http://www.biomedsearch.com/>
>
> This communication is confidential and may be subject to legal privilege.
> Nothing contained herein should be construed as legal or patenting advice.
>
>
> On Sat, Feb 22, 2014 at 3:15 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>> Yes, James, there is. It is no so much "bond" data, but structural data
>> involving from 2 to 4 atoms. To get this, simply use:
>>
>>
>> *minimize energy*
>>
>> *show minimization *
>> To understand the tables, I would direct you to MMFF MMFF94 Force Field
>> -- T. A. Halgren, J. Comp. Chem. 5 & 6 490-519ff (1996).
>>
>> Bob
>>
>>
>>
>> On Sat, Feb 22, 2014 at 10:32 AM, James <ja...@ryley.com> wrote:
>>
>>> Hi,
>>>
>>> If you minimize a structure, you end up with an energy, which is
>>> presumably the sum of all the bonds' variations from ideal lengths and
>>> angles (including torsion), plus any non-bonded forces involved (e.g., Van
>>> der Waals -- although I would think these end up being represented as
>>> changes in bonding also, since these forces must affect the bonds as they
>>> push/pull on things). Most programs, including Jmol, output this energy as
>>> a single total number for the molecule. But, it seems that the program
>>> must, in order to sum the energies, how each individual bond varies from
>>> what the force field would consider a 0 energy configuration.
>>>
>>> Is there a way to get at this data? For example, to list each bond, its
>>> reference angle and length, its actual angle and length (I know this can be
>>> accessed), and how much it contributes to the overall single point energy?
>>> Reference heat of formation would be nice too, if available, since that
>>> would let you calculate a percent change in bond energy rather than just
>>> the difference from 0, although it certainly isn't clear to me that the
>>> system even possesses that information.
>>>
>>> Sincerely,
>>> James Ryley, PhD, Patent Agent
>>> SumoBrain: Intellectual Property Solutions & Data
>>> AcclaimIP <https://www.acclaimip.com/> |
>>> FreePatentsOnline.com<http://www.freepatentsonline.com/>|
>>> SumoBrain.com <http://www.sumobrain.com/> |
>>> BioMedSearch.com<http://www.biomedsearch.com/>
>>>
>>> This communication is confidential and may be subject to legal privilege.
>>> Nothing contained herein should be construed as legal or patenting
>>> advice.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Managing the Performance of Cloud-Based Applications
>>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>>> Read the Whitepaper.
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Jmol-users mailing list
>>> Jmol-users@lists.sourceforge.net
>>> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Managing the Performance of Cloud-Based Applications
>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>> Read the Whitepaper.
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Jmol-users mailing list
>> Jmol-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 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
------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
