From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Feb 23 2013 - 02:30:10 CST
On Fri, Feb 22, 2013 at 11:31 PM, Stober, Spencer T
<spencer.t.stober_at_exxonmobil.com> wrote:
> Hello,
hello spence,
> I have performed a single point energy calculation in Gaussian (which I am
> not highly familiar with). I want to compare the energy results for this
> molecule with the results from a NAMD simulation of the same molecule in a
> vacuum using the CHARMM force field.
this is problematic, since the CHAMM force field is parameterized for
molecules in aqueous solution using the CHARMM specific variant of the
TIP3P water potential.
> So, for the NAMD run I have the standard output:
>
>
>
> ETITLE: TS BOND ANGLE DIHED IMPRP
>
> ELECT VDW BOUNDARY MISC KINETIC
>
> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
>
> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
>
>
> From this I need the VDW and ELECT energies for my calculations.
why?
>
> The output from the single point energy calculation from the Gaussian log
> file (for a single molecule) contains this as the energy:
>
>
>
> N-N= 2.091731426218D+03 E-N=-9.789529633567D+03 KE= 1.508520754068D+03
>
>
>
> I assume this is Nuclear-Nuclear, Electron-Nuclear, and Electron Kinetic
> energy.
>
>
>
> I would appreciate if anyone could comment on how the Gaussian output
> corresponds to the NAMD output. I.e., does N-N = VDW?, etc.
there is no such correspondence. you have two very different
hamiltonians with very different components.
about the only correlation that you have is between *total* energy
*differences*.
axel.
>
>
> Thanks for the help, Spence
>
>
>
>
>
>
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>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
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