From: Alessandro Cembran (cembran_at_chem.umn.edu)
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 Office: Univ. of Minnesota, Walter Library 117 Pleasant St SE, Room 473 Phone: +1 612-624-4617 E-mail: cembran_at_chem.umn.edu
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:24 CST