That's pretty much what I figured in terms of one value compensating for
another. In terms of total energy though, even that doesn't seem reliable,
at least not in real world terms of kcal/mol -- perhaps relative to other
values from the same force field it is fairly consistent. If only ab initio
calculations weren't so expensive. Thanks!
Sincerely,
James Ryley, PhD, Patent Agent
SumoBrain: Intellectual Property Solutions & Data
AcclaimIP <https://www.acclaimip.com/> |
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This communication is confidential and may be subject to legal privilege.
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On Mon, Feb 24, 2014 at 7:20 PM, Robert Hanson <[email protected]> wrote:
> 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 <[email protected]> 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 <[email protected]>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 <[email protected]> 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.
>>>>
>>>>
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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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>>
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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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