AMBER Archive (2000)

Subject: normal modes

From: hermone_at_pegasus.arc.nasa.gov
Date: Mon Nov 20 2000 - 17:51:55 CST

I am trying to do normal mode analysis for a large molecule. I minimized (
I thought ) to an rms of < .0001 but when I do the normal modes the rms
given is much higher. I have used binary input and output.
Here is the input:
  newton-raphson minimization test
 &data
     ntrun = 4, nsave=2, ndiag=2, cut=95.0, ibelly=0,
   alpha = 0.4, kform=2, ntxo=0, nprint=10,dielc = 4.0,smx = .01, emx = .01,
  ntx = 0, ntxo = 0, idiel = 0,
  drms = 0.0001, maxcyc=5000, bdwnhl=0.001, dfpred = 0.1,
     scnb=2.0, scee=1.2,
 &end
Here is the normal mode input
  obtain gas-phase normal modes
 &data
     ntrun = 1, nsave=20, ndiag=2, cut=95.0, ibelly=0, ntx=0,
     nprint=1, ioseen=0,ntxo = 0, alpha = 0.4,
     drms = 0.0001, maxcyc=1, bdwnhl=1.1, dfpred = 0.1,
     scnb=2.0, scee=1.2, idiel=0,
     nvect=1734,
 &end

here is the end of the minimization:

     F = -0.303100E+03 GRDMAX = 0.714861E-04 GNORM = 0.402570E-05
       E-NONB E-ELE E-HBOND E-BOND
    -0.44370E+03 -0.10722E+03 0.00000E+00 0.90599E+01
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.79254E+02 0.25146E+03 0.13039E+03 -0.22234E+03
       E-POL E-3BOD
Here is the end of the normal mode calculation:

     F = -0.129179E+04 GRDMAX = 0.152473E+02 GNORM = 0.292616E+01
       E-NONB E-ELE E-HBOND E-BOND
    -0.44370E+03 -0.42889E+03 0.00000E+00 0.90599E+01
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.79254E+02 0.25146E+03 0.13039E+03 -0.88937E+03
       E-POL E-3BOD
Maybe I'm not understanding the output of the minization. I don't want to
minimize indefinitely, though. Thank you very much for any help you can give.
Ann