**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Sat Feb 23 2013 - 02:30:10 CST

**Next message:**Jacqueline Schmidt: "center of mass calculation in the tcl interface"**Previous message:**Stober, Spencer T: "Single point energy calc with gaussian/namd... log file interpretation"**In reply to:**Stober, Spencer T: "Single point energy calc with gaussian/namd... log file interpretation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> not highly familiar with). I want to compare the energy results for this
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*> molecule with the results from a NAMD simulation of the same molecule in a
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*> vacuum using the CHARMM force field.
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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:
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*>
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*>
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*>
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*> ETITLE: TS BOND ANGLE DIHED IMPRP
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*>
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*> ELECT VDW BOUNDARY MISC KINETIC
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*>
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*> TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
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*>
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*> PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
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*>
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*>
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*>
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*> From this I need the VDW and ELECT energies for my calculations.
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why?

*>
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*> The output from the single point energy calculation from the Gaussian log
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*> file (for a single molecule) contains this as the energy:
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*>
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*>
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*>
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*> N-N= 2.091731426218D+03 E-N=-9.789529633567D+03 KE= 1.508520754068D+03
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*>
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*>
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*>
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*> I assume this is Nuclear-Nuclear, Electron-Nuclear, and Electron Kinetic
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*> energy.
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*>
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*>
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*>
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*> I would appreciate if anyone could comment on how the Gaussian output
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*> 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.

*>
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*>
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*> Thanks for the help, Spence
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*>
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*>
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*>
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*>
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*>
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*>
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*>
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*>
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-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.

**Next message:**Jacqueline Schmidt: "center of mass calculation in the tcl interface"**Previous message:**Stober, Spencer T: "Single point energy calc with gaussian/namd... log file interpretation"**In reply to:**Stober, Spencer T: "Single point energy calc with gaussian/namd... log file interpretation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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