AMBER Archive (2004)

Subject: AMBER: minimization output file format

From: Marsita M (
Date: Thu Aug 12 2004 - 12:51:35 CDT

dear amber users,

first and foremost, i am a beginner here, so my question is really the
basics for most of you here, and i would appreciate if someone can guide me
with the meanings of the minimization output file, such as:

    100 -1.3419E+04 1.7043E-01 1.6570E+01 CG 1012

BOND = 281.5388 ANGLE = 1182.3429 DIHED = 5309.2460
VDWAALS = -2823.1990 EEL = -33036.8393 EGB = -10465.3807
1-4 VDW = 1610.5875 1-4 EEL = 25129.8490 RESTRAINT = 0.6661
ESURF = 292.5711
EAMBER = -12519.3177

i was wondering what GMAX, NAME,NUMBER,ESURF stand for and what are the
significance of these terms in the result.
and all of these values are energy terms right.. in kcal/mol i suppose?

my second question is... is it common/ok to use both implicit and explicit
simulation for one system? say like.. for the minimization, i want to use
explicit MD, and the equilibration part, i would wish to use both implicit
and explicit MD simulation (say 20 ps implicit, and another 1ns explicit)..
is it acceptable to do that ? hope to hear from any of you.. thanks


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