**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
*

*> 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
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

-- 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 ]

*
This archive was generated by hypermail 2.1.6
: Wed Dec 31 2014 - 23:20:56 CST
*