AMBER Archive (2004)

Subject: AMBER: Spike in energy and RMS

From: Balvinder Singh (bvs_at_imtech.res.in)
Date: Wed Sep 08 2004 - 17:49:04 CDT


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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