Timeline for What does the "total energy" of a molecule mean for the Chem3D MM2 minimized energy calculation?
Current License: CC BY-SA 3.0
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| Aug 19, 2016 at 12:16 | history | edited | Wildcat | CC BY-SA 3.0 |
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| Aug 19, 2016 at 10:05 | history | edited | Wildcat | CC BY-SA 3.0 |
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| Aug 18, 2016 at 13:47 | comment | added | Deathbreath | The assumption of zeros at infinite separation are false for bonded potentials in force fields (which MM2 is). Take a closer look at the parametrization of force fields. Usually bonded potentials are zero at equilibrium. Hence you will get positive energies when these potentials are coupled while adding electrostatics can go either way. | |
| Aug 12, 2016 at 21:28 | comment | added | user7951 | The Chem3D manual confirms your definition of total energy as sum of kinetic energy and potential energy. However, the “Total Energy” reported by MM2 in Chem3D is actually the total steric energy, which is the sum of the individual terms for bond stretching, bond angle bending, torsion, van der Waals interactions, and electrostatic interactions. (I can reproduce the results given in the question with default values for MM2.) | |
| Aug 12, 2016 at 21:20 | comment | added | Nova | Perhaps the steric effects from the methyl groups as well as the repulsive effects from a higher electron density conjugated system contribute to the positive total energy? I'm sure nothing is wrong with the set up and even a simple MM2 model should be capable of approximating a positive or negative energy. | |
| Aug 12, 2016 at 19:29 | history | edited | Wildcat | CC BY-SA 3.0 |
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| Aug 12, 2016 at 19:24 | history | answered | Wildcat | CC BY-SA 3.0 |