I am minimizing a protein using AMBER 7 on IRIX platform. During
minimization, the energy sharply rises at a single step and then returns
to lower value on the very next step. Analysis shows bond and angle
energy increases sharply as compared to other energies. And this is
repeated at every 25th step. The output shows similar pattern of spike in
energy and RMS with IGB=one as well. However, at the end, the minimization
converges to a visually normal structure meeting convergence criteria.
Is this behaviour normal? Can anyone explain it?
-Balvinder
The input is as follows:
&cntrl
imin=1, maxcyc=65000, ncyc=12000, dielc=4,
drms=0.0005, ntb=0, cut=50, ntpr=1, ntwx=500, ntwr=500,
&end
&ewald
eedmeth=5,
&end
A part of the output:
..
..
..
NSTEP ENERGY RMS GMAX NAME NUMBER
21204 7.7982E+01 1.3034E-02 2.2445E-01 HH12 423
BOND = 24.0978 ANGLE = 97.6317 DIHED = 514.6982
VDWAALS = -544.7447 EEL = -370.6831 HBOND = 0.0000
1-4 VDW = 215.7988 1-4 EEL = 141.1831 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
21205 4.8300E+02 2.5692E+01 3.0659E+02 C 550
BOND = 349.9796 ANGLE = 167.3124 DIHED = 518.1113
VDWAALS = -542.3081 EEL = -369.2192 HBOND = 0.0000
1-4 VDW = 219.0747 1-4 EEL = 140.0487 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
21206 7.7981E+01 2.8785E-02 3.2231E-01 C 550
BOND = 24.1048 ANGLE = 97.6212 DIHED = 514.6983
VDWAALS = -544.7441 EEL = -370.6810 HBOND = 0.0000
1-4 VDW = 215.8008 1-4 EEL = 141.1812 RESTRAINT = 0.0000
..
..
..
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Received on Fri Sep 10 2004 - 13:25:59 PDT
