Minimization Lesson,
Output File Minimization Lesson,
Output File
DISCOVER Molecular Simulation Program Version: 95.0 Beta Date: Tue Nov 8 13:06:38 1994 User Name: marj Host Name: iris90 Host Type: iris ---------------------------------------------------------------- Licensed by BIOSYM Technologies to BIOSYM SAN DIEGO ---------------------------------------------------------------- NLS: License for Discover_Pgm Checked Out randomSeed is set to 328800The randomSeed variable is actually irrelevant to a simple minimization such as run in this tutorial lesson.
Line 7:BTCL> beginLines from the input file are printed in the output file, so that you have a permanent record of the calculation conditions.
INPUT FILES ___________ File Type Name --------- ---- Forcefield /ax10/bioroot/develop/release950/irix51r4/biosym_lib/cvff.xfrc Molecular data cyclo00.mdf Coordinate cyclo00.carThese were the default forcefield and molecule-specification files.
Line 10:BTCL> minimize \
iteration_limit = 300 movement_limit = 0.200 \
sd \
convergence = 1000.0 line_search_precision = 0.100 \
cg \
convergence = 10.0 method = polak \
line_search_precision = 0.100 \
newton \
convergence = 0.001 method = bfgs \
line_search_precision = 0.900 max_atoms = 200 \
final_convergence = 0.001 \
execute +before +after \
command = {print output \
+total_energy \
+total_nonbond_energy \
+coulomb_energy \
+vdw_energy \
+repulsive_vdw_energy \
+dispersive_vdw_energy \
+internal_energy \
+bond_energy \
+angle_energy \
+torsion_energy \
+oop_energy}
MOLECULAR TOPOLOGY
__________________
Number of molecules: 1
Number of residues: 5
Number of atoms: 61
Number of atom types: 12
Number of bonds: 62
Number of angles: 112
Number of torsions: 162
Number of out-of-planes: 13
FORCEFIELD OPTIONS
__________________
Name : cvff_nocross_nomorse
# of automatic parameters : 0
NONBOND ENERGY CUTOFFS
______________________
Cutoff (A) Spline Width (A) Buffer Width (A)
vdW 9.50 1.00 0.50
Coulomb 9.50 1.00 0.50
Summation method for vdW : Group based
Summation method for Coulomb : Group based
Dielectric : 1.00
Illustration
of cutoff, spline width, buffer width.
Nonbond Energy I
----------------
Step Tot. NB Coul. E. vdW E.
kcal/mol kcal/mol kcal/mol
instant instant instant
0 77.768 -42.250 120.018
10 173.109 -40.589 213.698
20 -30.175 -81.878 51.703
30 -20.551 -62.943 42.392
40 -27.371 -59.080 31.709
50 -33.055 -60.272 27.217
60 -32.409 -61.200 28.791
70 -32.143 -62.753 30.610
80 -33.836 -63.291 29.455
90 -39.531 -64.476 24.945
100 -38.690 -59.527 20.837
110 -39.729 -59.681 19.952
120 -39.374 -58.888 19.514
130 -36.653 -58.941 22.288
140 -36.869 -59.294 22.424
150 -36.465 -60.451 23.986
160 -36.068 -59.591 23.523
170 -37.366 -58.595 21.229
180 -35.900 -58.076 22.175
190 -36.481 -58.441 21.960
200 -37.437 -58.517 21.081
210 -36.462 -58.626 22.164
220 -37.415 -59.091 21.676
230 -38.725 -60.030 21.304
240 -41.306 -61.637 20.330
250 -40.515 -61.664 21.149
260 -40.187 -61.345 21.158
270 -40.767 -61.328 20.561
280 -40.372 -61.315 20.944
290 -40.432 -61.324 20.892
300 -40.433 -61.306 20.872
Nonbond Energy II
-----------------
Step D. vdW E. R. vdW E.
kcal/mol kcal/mol
instant instant
0 -94.404 214.422
10 -130.068 343.766
20 -97.092 148.795
30 -93.516 135.908
40 -87.203 118.912
50 -84.781 111.998
60 -85.773 114.564
70 -86.372 116.982
80 -84.401 113.856
90 -81.838 106.783
100 -79.847 100.685
110 -79.776 99.728
120 -80.910 100.424
130 -83.828 106.116
140 -84.145 106.570
150 -84.245 108.232
160 -83.632 107.155
170 -81.820 103.049
180 -83.429 105.604
190 -83.214 105.174
200 -82.402 103.483
210 -83.221 105.385
220 -82.586 104.262
230 -82.218 103.523
240 -81.490 101.820
250 -82.699 103.848
260 -83.027 104.186
270 -83.142 103.703
280 -83.345 104.288
290 -83.382 104.274
300 -83.380 104.252
Internal Energy I
-----------------
Step Tot. Int. Bond E. Angle E. Tor. E.
kcal/mol kcal/mol kcal/mol kcal/mol
instant instant instant instant
0 27555.071 27262.355 279.634 11.053
10 1133.213 540.714 519.921 56.779
20 377.251 46.093 254.054 63.797
30 186.426 24.634 100.807 50.593
40 126.818 17.509 55.897 51.280
50 99.343 14.327 44.891 39.040
60 91.614 13.870 39.706 36.215
70 88.928 11.308 42.899 32.496
80 89.010 11.997 49.044 26.079
90 91.975 14.913 54.432 21.616
100 87.719 17.101 51.359 18.169
110 85.637 16.612 49.188 18.642
120 82.952 14.878 46.452 20.194
130 77.438 13.091 43.712 19.334
140 75.238 11.704 45.141 17.387
150 72.798 11.188 43.778 16.840
160 69.829 12.048 42.598 14.641
170 69.199 12.211 41.399 14.696
180 65.458 11.178 39.567 14.035
190 64.578 10.421 39.767 13.670
200 64.300 10.682 38.998 13.780
210 62.485 10.186 38.160 13.315
220 62.709 10.312 38.022 13.593
230 63.271 10.286 38.447 13.727
240 64.203 11.277 37.974 14.273
250 60.198 9.234 35.440 14.716
260 58.320 9.461 34.365 13.918
270 58.354 9.572 34.313 13.899
280 57.825 9.390 33.960 13.898
290 57.855 9.413 34.124 13.739
300 57.852 9.394 34.065 13.818
Internal Energy II
------------------
Step Oop E. Tot. C.
kcal/mol kcal/mol
instant instant
0 2.029 0.000
10 15.798 0.000
20 13.307 0.000
30 10.393 0.000
40 2.132 0.000
50 1.086 0.000
60 1.822 0.000
70 2.226 0.000
80 1.891 0.000
90 1.013 0.000
100 1.090 0.000
110 1.194 0.000
120 1.428 0.000
130 1.301 0.000
140 1.007 0.000
150 0.992 0.000
160 0.543 0.000
170 0.893 0.000
180 0.678 0.000
190 0.720 0.000
200 0.840 0.000
210 0.824 0.000
220 0.782 0.000
230 0.810 0.000
240 0.679 0.000
250 0.808 0.000
260 0.576 0.000
270 0.570 0.000
280 0.576 0.000
290 0.579 0.000
300 0.575 0.000
Minimize: No convergence after 300 iterations
maximum derivative = 0.2386
Last method used = Quasi Newton (BFGS)
Total number of iterations = 300
Total number of function calls = 477
CPU time used = 23.62 seconds
MINIMIZATION ENERGY SUMMARY
___________________________
Initial Final
------- -----
Total Potential energy 27632.839589 17.418209
Internal 27555.071441 57.851608
bond 27262.355242 9.393775
angle 279.633906 34.064552
torsion 11.053495 13.818031
out_of_plane 2.028798 0.575251
cross 0.000000 0.000000
bond_bond 0.000000 0.000000
bond_angle 0.000000 0.000000
end_bond_torsion 0.000000 0.000000
middle_bond_torsion 0.000000 0.000000
angle_torsion 0.000000 0.000000
angle_angle_torsion 0.000000 0.000000
bond_bond_1_3 0.000000 0.000000
angle_angle 0.000000 0.000000
torsion_torsion 0.000000 0.000000
oop_oop 0.000000 0.000000
nonbond 77.768148 -40.433399
vdW 120.017745 20.872412
vdW_repulsive 214.421850 104.252256
vdW_dispersive -94.404104 -83.379844
electrostatic -42.249598 -61.305811
hydrogenbond 0.000000 0.000000
The above output is what you
specified with the Analyze/Output command.
Line 35:BTCL> writeFile coordinate filename = .cor Total time used by DISCOVER: 27.01 secs Completion date: Tue Nov 8 13:07:31 1994 Exiting Discover: status OK.
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