AMBER Archive (2004)

Subject: Re: AMBER: Output of sander

From: Harianto (harianto_at_mailer.sb.fsu.edu)
Date: Thu Dec 23 2004 - 14:36:27 CST

Dr Case,
I run ANAL program and part of the result is the following:

----------------------------------------------
           ENERGY CONTRIBUTION BY GROUPS

      GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
   EELNB HBOND CONSTRAINT TOTAL

        1 482.64 1547.47 1138.92 404.78 5328.81 -593.00
-9067.62 0.00 0.00 -757.992
        2 0.00 0.00 0.00 0.00 0.00 552.72
-5515.11 0.00 0.00 -4962.390
        3 0.00 0.00 0.00 0.00 0.00 11.68
-331.56 0.00 0.00 -319.874
   TOTAL 482.64 1547.47 1138.92 404.78 5328.81 -28.59
-14914.29 0.00 0.00 -6040.256

           BOND + ANGLE + DIHED INTERACTION ENERGY MATRIX

             1 2 3
     1 3169.030 0.000 0.000
     2 0.000 0.000 0.000
     3 0.000 0.000 0.000

           INDIVIDUAL GROUPS INTERACTION

      GROUP INTRA INTER TOTAL

          1 3169.03 0.00 3169.03
          2 0.00 0.00 0.00
          3 0.00 0.00 0.00

      TOTAL 3169.03 0.00 3169.03

           VDW (N-B + 1-4) INTERACTION ENERGY MATRIX

             1 2 3
     1 -171.699 -43.900 10.859
     2 -43.900 568.421 12.505
     3 10.859 12.505 0.000

           INDIVIDUAL GROUPS INTERACTION

      GROUP INTRA INTER TOTAL

          1 -171.70 -33.04 -204.74
          2 568.42 -31.40 537.03
          3 0.00 23.36 23.36

      TOTAL 396.72 -20.54 376.19
-------------------------------------------------

Now, BOND+ANGLE+DIHED interactiion energy matrix is obtained from
482.64+167.47+1138.92 = 3169.03, similarly for the other groups.

But for VdW interaction energy matrix (also that of ELECTROSTATIC, not
displayed) cannot be obtained by the same way, e.g :
404.78 -593.0 = -188.22 is not the same as -171.70 in the matrix.
Similarly for the other groups.

Can you explain it to me, or is there something wrong?
Thank you very much.

Regards,
Harianto.

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