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
Received on Wed Sep 04 2002 - 12:14:40 PDT
