AMBER Archive (2008)

Subject: AMBER: anal

From: Marina Grabar (Marina.Grabar_at_irb.hr)
Date: Mon May 19 2008 - 08:30:13 CDT

Hi,

I run anal program and my input is:
      NTX = 1 NTXO = 0 NRC = 0
      NRCX = 0 NGRPX = 3 KFORM = 1

      NTB = 0 BOXX = 0.000 BOXY = 0.000
      BOXZ = 0.000 BETA = 0.000

      NTF = 1 NTID = 0 NTN = 1
      NTNB = 0 NSNB = 50 IDIEL = 0

      RCUT = 15.00 SCNB = 2.00
      SCEE = 1.20 DIELC = 1.00

      IMAX EBMAX EANMAX EDIHMAX ENB14MAX
          1 20.00 20.00 20.00 200.00

      EEL14MAX ENBMAX EELMAX EHBMAX ECONSMAX
         50.00 1000.00 200.00 200.00 0.00

The part of the results is the following:

           ENERGY CONTRIBUTION BY GROUPS

      GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
    EELNB HBOND CONSTRAINT TOTAL

        1 4.61 19.17 8.30 35.98 -83.76 -40.79
    30.42 0.00 0.00 -26.061
        2 1.45 10.87 26.59 7.62 -57.31 -10.26
   -33.13 0.00 0.00 -54.177
        3 1113.63 0.00 0.00 0.00 0.00 2922.32
-20799.87 0.00 0.00 -16763.915
   TOTAL 1084.57 15.79 -41.63 21.42 -154.68 -17910.70
-20790.88 -8.00 6.56 -16869.158

           BOND + ANGLE + DIHED INTERACTION ENERGY MATRIX

             1 2 3
     1 32.076 0.000 0.000
     2 0.000 38.905 0.000
     3 0.000 0.000 1113.633

           INDIVIDUAL GROUPS INTERACTION

      GROUP INTRA INTER TOTAL

          1 32.08 0.00 32.08
          2 38.91 0.00 38.91
          3 1113.63 0.00 1113.63

      TOTAL 1184.61 0.00 1184.61

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

             1 2 3
     1 -20790.876 -8.000 -16869.158
     2 -8.000 6.560 -10.394
     3 -16869.158 -10.394 2940.020

           INDIVIDUAL GROUPS INTERACTION

      GROUP INTRA INTER TOTAL

          1 -20790.88 -16877.16 -37668.03
          2 6.56 -18.39 -11.84
          3 2940.02 -16879.55 -13939.53

      TOTAL -17844.30 -16887.55 -34731.85

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

             1 2 3
     1 1084.572 15.788 21.422
     2 15.788 -41.631 -154.677
     3 21.422 -154.677 -17910.699

           INDIVIDUAL GROUPS INTERACTION

      GROUP INTRA INTER TOTAL

          1 1084.57 37.21 1121.78
          2 -41.63 -138.89 -180.52
          3 -17910.70 -133.26 -18043.95

      TOTAL -16867.76 -117.47 -16985.23

I found the answer that the "energy contributions by groups" lists the INTRA +
(1/2) INTER as belonging to the group. But I don't get good results
for VdW and EEL interaction energy matrices . Where did I get wrong?

Thank you!
Marina 

-- 
Marina Grabar
Institute Rudjer Boskovic
Bijenicka 54
HR-10000, Zagreb
CROATIA

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu