From: Alessandro Cembran (
Date: Mon Feb 19 2007 - 11:36:16 CST


Does anybody know what's the difference among TOTAL, TOTAL2 and TOTAL3
energies in the NAMD output?
I realized that TOTAL is just the sum of all the listed contributions
(energies from tcl scripts are not added).
As far as I know, TOTAL3 should be more stable, but I do not know how
TOTAL2 and TOTAL3 are calculated.
Do they have anything to do with high frequencies adjustments? In CHARMM
there is an energy corrected for high frequency and I thought it might
also be the case in NAMD.
Anyway, if one wants to extract energy information from a trajectory to
build a PMF profile, what energy would be the correct one to use and why?



Alessandro Cembran,PhD
Post Doctoral Associate
Mailing Address:
Univ. of Minnesota, Dept. of Chemistry
G2, 139 Smith Hall 207 Pleasant St SE
Minneapolis, MN 55455-0431
Univ. of Minnesota, Walter Library
117 Pleasant St SE, Room 473
Phone: +1 612-624-4617

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