Positive values of Energy (python)

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Positive values of Energy (python)

Filip Stefaniak
Hi All,

I'm trying to calculate Energy values for a set of small molecules in
python. It is basically calculated like here:


[...]
ff = openbabel.OBForceField.FindForceField('GAFF')
ff.Setup(mol)
print ff.Energy()


I've tried for several sets of conformers (X-ray, minimized, 2D),
various input formats (sdf, mol2) and various forcefields and in most
cases I get the positive values of the Total Energy. Is it OK? The trend
is correct (more optimal geometries has lower energies than not optimal
geometries) but still, I would assume to get negative values for good
conformers.

Here is a bunch of statistics for the Total Energy calculated for
optimized set of small molecules using the GAFF forcefield:

             count    9915
             mean     243.754647
             std      137.775753
             min     -160.229365
             25%      137.313904
             50%      236.810371
             75%      307.166353
             max      760.573306


Any comments, clues  or answers if such energy ranges/values are OK are
welcome.

bests,
Filip


--
Filip Stefaniak
Uptime: 13667 dni 15 godzin
W lodówce ma 7.0stC, na działce w sadku 6.8stC

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Positive values of Energy (python)

Geoff Hutchison
While GAFF, MMFF94 and other force fields attempt to replicate heats of formation, the heat for formation of an organic molecule need not always be negative.

(Consider, for example cyclobutane, which is perfectly stable but has a positive DeltaG.)
https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/energy1.htm

Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [hidden email]
web: http://hutchison.chem.pitt.edu/

> I've tried for several sets of conformers (X-ray, minimized, 2D),
> various input formats (sdf, mol2) and various forcefields and in most
> cases I get the positive values of the Total Energy. Is it OK? The trend
> is correct (more optimal geometries has lower energies than not optimal
> geometries) but still, I would assume to get negative values for good
> conformers.


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Positive values of Energy

homeopathynews
This post was updated on .
In reply to this post by Filip Stefaniak
Energy is important and it is used in all of the above other fields.Energy and power system is an important subjects of the system it is used in energy utilities.homeopathy consultation india
Loading...