AMBER Archive (2002)

Subject: how to detect bad contact?

From: X. Tan (xjtan_at_u.washington.edu)
Date: Wed Sep 04 2002 - 14:14:40 CDT

Hi, dear all

In my simulation, I found the the vdw energy always have a larger
(10-30 kcal/mol) fluctuation than the Etot, EPtot..., I guess there might
be some bad contact in my system. I know anal module can handle this task,
so I performed a test run. My input and output file are as below.

-----------------------------------
bad contact
    1 0 0 0 4 1
    2 77.5600148 58.8258741 63.9357306 90.0
    2 0 2 1 9999 1
 10.0 2.0 1.2 1.0
 0
PDB
ENERGY
GROUP1
RES 1 103
END
GROUP2
RES 104 206
END
GROUP3
RES 207 207
END
GROUP4 RES 208 8882
END
END
STOP
-----------------------------------
.....
          INITIAL ENERGY COMPONENTS

     TOTAL ENERGY = -41055.4980
     NON-BONDED VDW ENERGY = 3498.4034
     NON-BONDED EEL ENERGY = -58667.9516
     HBOND 10-12 ENERGY = 0.0000
     BOND ENERGY = 615.6586
     ANGLE ENERGY = 1608.8765
     DIHEDRAL ENERGY = 2093.3826
     NON-BOND 14 VDW ENERGY = 758.2359
     NON-BOND 14 EEL ENERGY = 9037.8967
     BOND CONSTRAINT ENERGY = 0.0000
     ANGLE CONSTRAINT ENERGY = 0.0000
     DIHEDRAL CONSTRAINT ENERGY = 0.0000
     POSITION CONSTRAINT ENERGY = 0.0000

          ENERGY CONTRIBUTION BY GROUPS
     GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB
EELNB HBOND CONSTRAINT TOTAL
       1 298.21 776.13 1044.28 380.83 4490.50 -869.67
-8806.38 0.00 0.00 -2686.089
       2 304.75 822.00 1028.58 367.72 4382.54 -905.88
-8814.92 0.00 0.00 -2815.224
       3 12.70 10.75 20.52 9.69 164.86 -15.82
-145.83 0.00 0.00 56.863
       4 0.00 0.00 0.00 0.00 0.00 5292.34
-40900.33 0.00 0.00 -35607.988
  TOTAL 615.66 1608.87 2093.38 758.24 9037.90 3500.96
-58667.45 0.00 0.00 -41052.438

          BOND + ANGLE + DIHED INTERACTION ENERGY MATRIX
            1 2 3 4
    1 2118.628 0.000 0.000 0.000
    2 0.000 2155.322 0.000 0.000
    3 0.000 0.000 43.966 0.000
    4 0.000 0.000 0.000 0.000

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL
         1 2118.63 0.00 2118.63
         2 2155.32 0.00 2155.32
         3 43.97 0.00 43.97
         4 0.00 0.00 0.00
     TOTAL 4317.92 0.00 4317.92

          VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
            1 2 3 4
    1 -359.338 -117.208 -24.453 -120.027
    2 -117.208 -384.316 -2.990 -189.685
    3 -24.453 -2.990 7.388 0.393
    4 -120.027 -189.685 0.393 5447.270

          INDIVIDUAL GROUPS INTERACTION
     GROUP INTRA INTER TOTAL
         1 -359.34 -261.69 -621.03
         2 -384.32 -309.88 -694.20
         3 7.39 -27.05 -19.66
         4 5447.27 -309.32 5137.95
     TOTAL 4711.00 -453.97 4257.03

          ELECTROSTATIC (N-B + 1-4) INTERACTION ENERGY MATRIX
            1 2 3 4
    1 -3104.234 -262.931 -56.418 -2103.490
    2 -262.931 -3142.193 -4.596 -2312.896
    3 -56.418 -4.596 53.884 -8.685
    4 -2103.490 -2312.896 -8.685 -38688.707

          INDIVIDUAL GROUPS INTERACTION

     GROUP INTRA INTER TOTAL
         1 -3104.23 -2422.84 -5527.07
         2 -3142.19 -2580.42 -5722.62
         3 53.88 -69.70 -15.82
         4 -38688.71 -4425.07 -43113.78
     TOTAL -44881.25 -4749.02 -49630.27

          HBOND INTERACTION ENERGY MATRIX
            1 2 3 4
    1 0.000 0.000 0.000 0.000
    2 0.000 0.000 0.000 0.000
    3 0.000 0.000 0.000 0.000
    4 0.000 0.000 0.000 0.000

          INDIVIDUAL GROUPS INTERACTION
     GROUP INTRA INTER TOTAL
         1 0.00 0.00 0.00
         2 0.00 0.00 0.00
         3 0.00 0.00 0.00
         4 0.00 0.00 0.00
     TOTAL 0.00 0.00 0.00

          TOTAL INTERACTION ENERGY MATRIX

            1 2 3 4
    1 -1344.944 -380.139 -80.871 -2223.517
    2 -380.139 -1371.187 -7.586 -2502.582
    3 -80.871 -7.586 105.238 -8.292
    4 -2223.517 -2502.582 -8.292 -33241.438

          INDIVIDUAL GROUPS INTERACTION
     GROUP INTRA INTER TOTAL
         1 -1344.94 -2684.53 -4029.47
         2 -1371.19 -2890.31 -4261.49
         3 105.24 -96.75 8.49
         4 -33241.44 -4734.39 -37975.83
     TOTAL -35852.33 -5202.99 -41055.32
---------------------------------------------------------
My question is how to find bad contact from the output information? And it
is right way to do that? Thanks for your time.

Xiaojian