AMBER: the energy difference between sander and nmode

From: xiaowei li <xl3a.virginia.edu>
Date: Fri, 12 Nov 2004 16:52:57 -0500

Dear AMBER users:
    I have used SANDER (amber 8) and NMODE (amber 7) to minimize the
energy of poly[C]-poly[G] RNA with 12 base pairs without sodium ions. It
seems to me that the energies after minimization are different.
Therefore, the calcualted normal modes are different for both cases. I
am not sure whether it is because of the version differences, or the
differnt methods used to minimize the energy in SANDER and NMODE, or
because I have made mistakes to set the control flags. Thank you for
your help very much.

Input file for energy minimization using SANDER
&cntrl
   imin=1,
   maxcyc=10000000,
   ncyc=550000,
   ntb=0,
   igb=0,
   cut=99.0,
   dielc=1,
   ntpr=100,
   drms=0.0001,
   ntxo=0,
   scee=2.0,
&end
&ewald
  eedmeth=5
&end

Final Energy after mininization using SANDER

   step = 0
      F = -0.904190E+03 GRDMAX = 0.677208E-03 GNORM = 0.996493E-04
        E-NONB E-ELE E-HBOND E-BOND
     -0.39704E+03 -0.73444E+03 0.00000E+00
0.28200E+02
        E-ANGLE E-DIHED E-NB14 E-EEL14
      0.14261E+03 0.54218E+03 0.25738E+03
-0.74308E+03
        E-POL E-3BOD
      0.00000E+00 0.00000E+00

The input file for energy minimization using NMODE

&data
      ntrun=4,
      nsave=1,
      ndiag=2,
      cut=99.0,
      nprint=10,
      drms=0.0001,
      maxcyc=80000,
      scnb=2.0,
      scee=2.0,
      ntxo=0,
  &end

The energy after minimization using NMODE

   step = 0
      F = -0.890503E+03 GRDMAX = 0.690726E-03 GNORM = 0.999473E-04
        E-NONB E-ELE E-HBOND E-BOND
     -0.36385E+03 -0.69668E+03 0.00000E+00
0.27845E+02
        E-ANGLE E-DIHED E-NB14 E-EEL14
      0.11832E+03 0.55368E+03 0.23530E+03
-0.76512E+03
        E-POL E-3BOD
      0.00000E+00 0.00000E+00


-- 
David (Xiaowei) Li
Charles L. Brown Electrical and Computer Engineering
University of Virginia
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Received on Fri Nov 12 2004 - 22:53:00 PST
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