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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