| Chapter 30. Simulated Annealing Search for Multiple Minima (ANNEAL) | ||
|---|---|---|
|
Part II. AMPAC™ 10 Examples |  |
| Chapter 30. Simulated Annealing Search for Multiple Minima (ANNEAL) | ||
|---|---|---|
|
|
Part II. AMPAC™ 10 Examples | |
Table of Contents
The cyclohexane molecule has been chosen as an example of using simulated annealing on a molecule with relatively low rotational barriers. There are four conformers of the molecule that can be identified (chair, boat (flexible), twist or skew boat, and half-chair) and all of these are located by AMPAC’s annealing protocol, using relaxed constraints and limited penalty functions.
am1 rhf singlet t=auto anneal truste pen2 ncheck=10 noxyz limit Cyclohexane Annealing on cyclic system: PEN2, NCHECK, LIMIT C 0.000000 0 0.000000 0 0.000000 0 0 0 0 C 1.520880 0 0.000000 0 0.000000 0 1 0 0 C 1.520880 0 112.706930 1 0.000000 0 2 1 0 C 1.520880 0 112.706930 1 -7.376720 1 3 2 1 C 1.520880 0 112.706930 1 -46.310020 1 1 2 3 C 1.520880 0 112.706930 1 50.819480 1 5 1 2 H 1.121200 0 112.384140 1 75.006870 1 1 2 3 H 1.121200 0 112.384140 1 -167.313050 1 1 2 3 H 1.121200 0 112.384140 1 121.019560 1 2 3 1 H 1.121200 0 112.384140 1 -121.144800 1 2 3 1 H 1.121200 0 112.384140 1 113.455200 1 3 2 1 H 1.121200 0 112.384140 1 -128.802830 1 3 2 1 H 1.121200 0 112.384140 1 177.862400 1 4 3 2 H 1.121200 0 112.384140 1 -63.807980 1 4 3 2 H 1.121200 0 112.384140 1 57.505850 1 5 4 3 H 1.121200 0 112.384140 1 -154.797280 1 5 4 3 H 1.121200 0 112.384140 1 121.566360 1 6 5 4 H 1.121200 0 112.384140 1 -122.040500 1 6 5 4 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 $$ limit - annealing boundaries100 100 -180 100 -180 100 -180 100 -180 100 -180 100 -180 100
-180 100 -180 100 -180 100 -180 100 -180 100 -180 100 -180 100 -180 100 -180 130 130 180 130 180 130 180 130 180 130 180 130 180 130
180 130 180 130 180 130 180 130 180 130 180 130 180 130 180 130 180 $$ end of extra data
|
This is the extra input section marker for reaction path data. Note, that this marker can be shortened to “$$ limit”. Details of these markers are found in the section called “Extra Input Data”. |
|
|
These are the lower boundaries of the bond angles and dihedrals (in order as specified) as required for by the annealing keyword LIMIT. |
|
|
These are the upper boundaries of the bond angles and dihedrals (in order as specified) as required for by the annealing keyword LIMIT. |
Timestamp: 2011-08-31-12-30-05-000000059C-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C6H12
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -38.461667 kcal
= -160.962076 kJ
ELECTRONIC ENERGY = -4336.156767 eV
CORE-CORE REPULSION = 3401.263230 eV
TOTAL ENERGY = -934.893537 eV
GRADIENT NORM = 0.142334
RMS GRADIENT NORM = 0.025564
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 10.922850 eV
HOMO-LUMO GAP = 14.591989 eV
DIPOLE = 0.001011 debyes
MOLECULAR WEIGHT = 84.160800
MOLECULAR POINT GROUP = C2h 0.100000
NO. OF FILLED LEVELS = 18 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 36
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE PEN2 NCHECK=10 NOXYZ LIMIT
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.1551
C 1.520880 0 0.000000 0 0.000000 0 1 0 0 -0.1551
C 1.520880 0 111.123665 1 0.000000 0 2 1 0 -0.1552
C 1.520880 0 111.132186 1 55.517365 1 3 2 1 -0.1547
C 1.520880 0 111.125824 1 -55.553493 1 1 2 3 -0.1552
C 1.520880 0 111.136222 1 55.514987 1 5 1 2 -0.1547
H 1.121200 0 109.556127 1 -176.750967 1 1 2 3 0.0769
H 1.121200 0 109.417071 1 65.389211 1 1 2 3 0.0782
H 1.121200 0 109.553009 1 121.190059 1 2 3 1 0.0769
H 1.121200 0 109.422604 1 -120.947750 1 2 3 1 0.0782
H 1.121200 0 109.415490 1 -65.433537 1 3 2 1 0.0782
H 1.121200 0 109.548147 1 176.714592 1 3 2 1 0.0769
H 1.121200 0 109.447594 1 -176.943500 1 4 3 2 0.0767
H 1.121200 0 109.309974 1 65.465345 1 4 3 2 0.0781
H 1.121200 0 143.756993 1 -124.603119 1 5 4 3 0.0769
H 1.121200 0 93.045319 1 109.416516 1 5 4 3 0.0782
H 1.121200 0 109.312266 1 121.079425 1 6 5 4 0.0781
H 1.121200 0 109.449883 1 -121.329555 1 6 5 4 0.0767
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-08-31-12-30-05-000000059C-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C6H12
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -35.291044 kcal
= -147.693018 kJ
ELECTRONIC ENERGY = -4341.347862 eV
CORE-CORE REPULSION = 3406.591814 eV
TOTAL ENERGY = -934.756048 eV
GRADIENT NORM = 0.042607
RMS GRADIENT NORM = 0.007653
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 10.673743 eV
HOMO-LUMO GAP = 14.347769 eV
DIPOLE = 0.000661 debyes
MOLECULAR WEIGHT = 84.160800
MOLECULAR POINT GROUP = D2 0.100000
NO. OF FILLED LEVELS = 18 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 36
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE PEN2 NCHECK=10 NOXYZ LIMIT
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.1535
C 1.520880 0 0.000000 0 0.000000 0 1 0 0 -0.1540
C 1.520880 0 112.213976 1 0.000000 0 2 1 0 -0.1535
C 1.520880 0 111.557704 1 -29.939332 1 3 2 1 -0.1532
C 1.520880 0 111.555172 1 -30.142091 1 1 2 3 -0.1535
C 1.520880 0 111.567720 1 62.750572 1 5 1 2 -0.1537
H 1.121200 0 109.547324 1 90.596059 1 1 2 3 0.0780
H 1.121200 0 109.613700 1 -151.717220 1 1 2 3 0.0766
H 1.121200 0 109.706537 1 121.281831 1 2 3 1 0.0758
H 1.121200 0 108.982281 1 -121.704820 1 2 3 1 0.0759
H 1.121200 0 109.543428 1 90.800513 1 3 2 1 0.0780
H 1.121200 0 109.613276 1 -151.513979 1 3 2 1 0.0766
H 1.121200 0 109.524036 1 -175.444429 1 4 3 2 0.0765
H 1.121200 0 108.888901 1 -58.295232 1 4 3 2 0.0779
H 1.121200 0 106.591923 1 51.245628 1 5 4 3 0.0780
H 1.121200 0 137.681082 1 -166.343590 1 5 4 3 0.0766
H 1.121200 0 109.636356 1 121.386734 1 6 5 4 0.0758
H 1.121200 0 108.895532 1 -121.788786 1 6 5 4 0.0758
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-08-31-12-30-05-000000059C-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Aug-31-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C6H12
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = 68.531095 kcal
= 286.802633 kJ
ELECTRONIC ENERGY = -4203.135787 eV
CORE-CORE REPULSION = 3272.881804 eV
TOTAL ENERGY = -930.253983 eV
GRADIENT NORM = 0.084387
RMS GRADIENT NORM = 0.015156
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 7.475143 eV
HOMO-LUMO GAP = 7.408058 eV
DIPOLE = 0.602974 debyes
MOLECULAR WEIGHT = 84.160800
MOLECULAR POINT GROUP = C1 0.100000
NO. OF FILLED LEVELS = 18 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 36
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE PEN2 NCHECK=10 NOXYZ LIMIT
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.1569
C 1.520880 0 0.000000 0 0.000000 0 1 0 0 -0.1487
C 1.520880 0 112.136196 1 0.000000 0 2 1 0 -0.1140
C 1.520880 0 116.144031 1 -91.587285 1 3 2 1 -0.3274
C 1.520880 0 111.503480 1 -49.763632 1 1 2 3 -0.1524
C 1.520880 0 109.788080 1 50.544477 1 5 1 2 -0.2933
H 1.121200 0 109.470583 1 -171.367561 1 1 2 3 0.0805
H 1.121200 0 109.094858 1 70.946977 1 1 2 3 0.0824
H 1.121200 0 109.282892 1 121.458833 1 2 3 1 0.0941
H 1.121200 0 108.735837 1 -121.019887 1 2 3 1 0.0821
H 1.121200 0 103.633653 1 24.070103 1 3 2 1 0.1761
H 1.121200 0 115.256379 1 131.780579 1 3 2 1 0.1171
H 1.121200 0 119.553416 1 23.861674 1 4 3 2 0.1187
H 1.121200 0 119.257474 1 -164.337223 1 4 3 2 0.1173
H 1.121200 0 122.158441 1 -0.070768 1 5 4 3 0.0767
H 1.121200 0 130.053071 1 177.265616 1 5 4 3 0.0810
H 1.121200 0 113.879260 1 -138.731518 1 6 5 4 0.0821
H 1.121200 0 113.577996 1 91.432352 1 6 5 4 0.0846
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-08-31-12-30-05-000000059C-win64
User Info: John Millam, Nahum,
*******************************************************************************
AM1 CALCULATION RESULTS
*******************************************************************************
* AMPAC Version 10.0.1
* Presented by:
*
* Semichem, Inc.
* www.semichem.com
*
* AM1 - THE AM1 HAMILTONIAN TO BE USED
* RHF - RESTRICTED HARTREE-FOCK CALCULATION
* ANNE - SIMULATED ANNEALING ON ENERGY ONLY
* TRUSTE - MINIMIZE ENERGY USING TRUST REGION METHOD
* NOXYZ - CARTESIAN COORDINATES NOT TO BE PRINTED
* T=AUTO - AUTOMATIC DETERMINATION OF ALLOWED TIME
* SINGLET - IS THE REQUIRED SPIN MULTIPLICITY
*******************************************************************************
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE PEN2 NCHECK=10 NOXYZ LIMIT
Cyclohexane
Annealing on cyclic system: PEN2, NCHECK, LIMIT
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.52088 1
3 C 1.52088 112.70693 * 2 1
4 C 1.52088 112.70693 * -7.37672 * 3 2 1
5 C 1.52088 112.70693 * -46.31002 * 1 2 3
6 C 1.52088 112.70693 * 50.81948 * 5 1 2
7 H 1.12120 112.38414 * 75.00687 * 1 2 3
8 H 1.12120 112.38414 * -167.31305 * 1 2 3
9 H 1.12120 112.38414 * 121.01956 * 2 3 1
10 H 1.12120 112.38414 * -121.14480 * 2 3 1
11 H 1.12120 112.38414 * 113.45520 * 3 2 1
12 H 1.12120 112.38414 * -128.80283 * 3 2 1
13 H 1.12120 112.38414 * 177.86240 * 4 3 2
14 H 1.12120 112.38414 * -63.80798 * 4 3 2
15 H 1.12120 112.38414 * 57.50585 * 5 4 3
16 H 1.12120 112.38414 * -154.79728 * 5 4 3
17 H 1.12120 112.38414 * 121.56636 * 6 5 4
18 H 1.12120 112.38414 * -122.04050 * 6 5 4
MOLECULAR POINT GROUP SYMMETRY CRITERIA
C1 0.10000000
SINGLET STATE CALCULATION
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 18
** REFERENCES TO PARAMETERS **
H (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
C (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
*******************************************************************************
* KEYWORDS DEDICATED TO SIMULATED ANNEALING SECTION
*
* LIMIT - EXPLICIT PERIODIC CONDITIONS GIVEN
* NCHECK= - SET MARKOV CHAIN IN PIECES OF 10 LONG
* PEN2 - SWITCH ON MIN/MAX PENALTY ON INTERATOMIC DISTANCES
* - PENALTIES OPERATED BY SKEWED REBOUNDS
*******************************************************************************
STANDARD DEVIATION ON ENERGY (KCAL) 0.00000055521
STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD) 0.00000000 0.00018717 0.00016811
SIMULATED ANNEALING BY METROPOLIS SCHEME IN 31 VARIABLES
VERSION 2.0 (MAY 2000)
THERMALIZATION THRESHOLD ON COST FNCT 0.080
MAXIMUM STEP SIZE 2.00000
CONVERGENCE CRITERION ON STEP SIZE 0.06325
MAXIMUM NUMBER OF STEPS AT EACH TEMPERATURE 1000
FIRST TEMPERATURE (HOT) SET TO 200.00
TEMPERATURE EXPONENTIAL DECAY 0.80
LAST TEMPERATURE (COLD) SET TO 2.00
RANDOM SEQUENCE INITIATOR -9876543
MARKOV CHAIN STUDIED BY PIECES OF 10
No OF TEMPERATURES TO DETECT A FROZEN SYSTEM 2
EQUIVALENCE THRESHOLD IN CLUSTERING ANALYSIS 1.00
BAND-PASS FILTER NO 1 CENTERED AT 1.40 ANGSTROMS
HALF BAND-WIDTH 13.50 %
CAN HOLD 250 CANDIDATES FOR QUENCHING.
PENALTIES ACTIVATED:
ON CHEMICAL BONDS, THRESHOLD: 0.20
PERIODIC BOUNDARY CONDITIONS (ANGSTROMS, DEGREES)
LOWER BOUND 100.0000 100.0000 -180.0000 100.0000 -180.0000 100.0000 
-180.0000 100.0000 -180.0000 100.0000 -180.0000 100.0000
-180.0000 100.0000 -180.0000 100.0000 -180.0000 100.0000
-180.0000 100.0000 -180.0000 100.0000 -180.0000 100.0000
-180.0000 100.0000 -180.0000 100.0000 -180.0000 100.0000
-180.0000
TRIAL COORD 112.7069 112.7069 -7.3767 112.7069 -46.3100 112.7069
50.8195 112.3841 75.0069 112.3841 -167.3131 112.3841
121.0196 112.3841 -121.1448 112.3841 113.4552 112.3841
-128.8028 112.3841 177.8624 112.3841 -63.8080 112.3841
57.5059 112.3841 -154.7973 112.3841 121.5664 112.3841
-122.0405
UPPER BOUND 130.0000 130.0000 180.0000 130.0000 180.0000 130.0000
180.0000 130.0000 180.0000 130.0000 180.0000 130.0000
180.0000 130.0000 180.0000 130.0000 180.0000 130.0000
180.0000 130.0000 180.0000 130.0000 180.0000 130.0000
180.0000 130.0000 180.0000 130.0000 180.0000 130.0000
180.0000
COST FNCT IS ENERGY (KCAL/MOLE)
PENALTY FUNCTION FOR LOCATION OF BONDS AND DETAILED MINIMUM DISTANCE CHECK 
IS INITIALIZED WITH TOLERANCE 0.200
LOCATED BONDS BETWEEN THE FOLLOWING ATOMS:
123456789012345678
1 .*..*.**..........
2 *.*.....**........
3 .*.*......**......
4 ..*..*......**....
5 *....*........**..
6 ...**...........**
7 *.................
8 *.................
9 .*................
0 .*................
1 ..*...............
2 ..*...............
3 ...*..............
4 ...*..............
5 ....*.............
6 ....*.............
7 .....*............
8 .....*............
VISIT OF THE PES BY SIMULATED ANNEALING
---------------------------------------
UNABLE TO HAVE 5 ACCEPTED MOVE-UP AFTER 1001 CALLS
AT TEMPERATURE 21.4748 WITH STEP 0.0000
ANNEALING STOPPED AT THIS POINT. EITHER THE SYSTEM IS "FROZEN" OR POOR CHOICE IN STEP/TEMPERATURE
ELAPSED TIME IN ANNEALING 25.51 SECONDS
CLUSTERING ANALYSIS OF CONFORMATIONS
------------------------------------
KEEP 83 CONFORMATIONS FROM 91 SELECTED AT PES VISIT
QUENCHING OF REMAINING CONFORMATIONS
------------------------------------
PERFORMED WITHOUT PERIODIC BOUNDARIES.
PERFORMED WITHOUT PENALTIES ON INTERATOMIC DISTANCES.
MINIMIZE ENERGY BY TRUST ALGORITHM
QUENCHING No 1 -- STAGE 1 OF 1 ( 0.27 SECONDS)
..................................................
HEAT OF FORMATION = -35.291044 KCAL
RMS GRADIENT NORM = 0.007649 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
112.2140 111.5577 -29.9393 111.5552 -30.1421 111.5677 62.7506 109.5473
90.5961 109.6137 -151.7172 109.7065 121.2818 108.9823 -121.7048 109.5434
90.8005 109.6133 -151.5140 109.5240 184.5556 108.8889 -58.2952 106.5919
51.2456 137.6811 -166.3436 109.6364 121.3867 108.8955 -121.7888
QUENCHING No 2 -- STAGE 1 OF 1 ( 0.41 SECONDS)
..................................................
HEAT OF FORMATION = -38.461667 KCAL
RMS GRADIENT NORM = 0.025554 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
111.1237 111.1322 55.5174 111.1258 -55.5535 111.1362 55.5150 109.5561
-176.7510 109.4171 65.3892 109.5530 121.1901 109.4226 -120.9477 109.4155
-65.4335 109.5481 176.7146 109.4476 -176.9435 109.3100 65.4653 143.7570
-124.6031 93.0453 109.4165 109.3123 121.0794 109.4499 -121.3296
QUENCHING No 3 -- STAGE 1 OF 1 ( 0.20 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 4 -- STAGE 1 OF 1 ( 0.17 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 5 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 6 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 7 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 8 -- STAGE 1 OF 1 ( 0.27 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 9 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 10 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 11 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 12 -- STAGE 1 OF 1 ( 0.22 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 13 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 14 -- STAGE 1 OF 1 ( 0.09 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 15 -- STAGE 1 OF 1 ( 0.11 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 16 -- STAGE 1 OF 1 ( 0.20 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 17 -- STAGE 1 OF 1 ( 0.31 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 18 -- STAGE 1 OF 1 ( 0.30 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 19 -- STAGE 1 OF 1 ( 0.20 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 20 -- STAGE 1 OF 1 ( 0.37 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 21 -- STAGE 1 OF 1 ( 0.11 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 22 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 23 -- STAGE 1 OF 1 ( 0.17 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 24 -- STAGE 1 OF 1 ( 0.97 SECONDS)
..................................................
HEAT OF FORMATION = -35.291035 KCAL
RMS GRADIENT NORM = 0.025015 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
112.2138 111.5576 30.0098 111.5535 30.0724 111.5631 -62.7607 109.5484
-90.6631 109.6192 -208.3532 108.9777 121.7044 109.6993 -121.2854 109.5442
-90.7324 109.6102 -208.4130 109.5210 175.4489 108.8859 58.3048 106.5416
-51.2505 137.7190 166.3915 108.8946 121.7940 109.6349 -121.3897
QUENCHING No 25 -- STAGE 1 OF 1 ( 0.59 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 26 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 27 -- STAGE 1 OF 1 ( 0.30 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 28 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 29 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 30 -- STAGE 1 OF 1 ( 0.27 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 31 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 32 -- STAGE 1 OF 1 ( 0.23 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 33 -- STAGE 1 OF 1 ( 0.11 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 34 -- STAGE 1 OF 1 ( 0.36 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 35 -- STAGE 1 OF 1 ( 0.17 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 36 -- STAGE 1 OF 1 ( 0.19 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 37 -- STAGE 1 OF 1 ( 0.12 SECONDS)
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HEAT OF FORMATION = 68.531095 KCAL
RMS GRADIENT NORM = 0.015153 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
112.1362 116.1440 -91.5873 111.5035 -49.7636 109.7881 50.5445 109.4706
-171.3676 109.0949 70.9470 109.2829 121.4588 108.7358 -121.0199 103.6337
24.0701 115.2564 131.7806 119.5534 23.8617 119.2575 -164.3372 122.1584
-0.0708 130.0531 177.2656 113.8793 221.2685 113.5780 91.4324
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HEAT OF FORMATION = 68.531180 KCAL
RMS GRADIENT NORM = 0.030797 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
112.1181 116.1450 -91.5508 111.5093 -49.8453 109.7975 50.4736 109.4799
-171.4737 109.0840 70.8403 109.2817 121.4621 108.7431 -121.0227 103.6204
24.1460 115.2582 131.7831 119.5474 23.7629 119.2604 -164.4645 129.9558
177.1868 122.2623 -0.2062 113.8614 221.4050 113.6011 91.5556
QUENCHING No 83 -- STAGE 1 OF 1 ( 0.22 SECONDS)
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* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
TIME CONSUMPTION OF STAGE 1: 21.39 SECONDS
ON 5 POINTS AT END OF STAGE 1, 3 FULFILL STATIONARITY AND ENERGETIC REQUESTS.
DETAILS ON NON EQUIVALENT CRITICAL POINTS FOUND (ENERGY SORTED) 
---------------------------------------------------------------
CRITICAL POINT No 1
....................
HEAT OF FORMATION = -38.461667 KCAL
RMS GRADIENT NORM = 0.025554 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = C2h 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.52088 1
3 C 1.52088 111.12367 * 2 1
4 C 1.52088 111.13219 * 55.51736 * 3 2 1
5 C 1.52088 111.12582 * -55.55349 * 1 2 3
6 C 1.52088 111.13622 * 55.51499 * 5 1 2
7 H 1.12120 109.55613 * -176.75097 * 1 2 3
8 H 1.12120 109.41707 * 65.38921 * 1 2 3
9 H 1.12120 109.55301 * 121.19006 * 2 3 1
10 H 1.12120 109.42260 * -120.94775 * 2 3 1
11 H 1.12120 109.41549 * -65.43354 * 3 2 1
12 H 1.12120 109.54815 * 176.71459 * 3 2 1
13 H 1.12120 109.44759 * -176.94350 * 4 3 2
14 H 1.12120 109.30997 * 65.46534 * 4 3 2
15 H 1.12120 143.75699 * -124.60312 * 5 4 3
16 H 1.12120 93.04532 * 109.41652 * 5 4 3
17 H 1.12120 109.31227 * 121.07942 * 6 5 4
18 H 1.12120 109.44988 * -121.32956 * 6 5 4
CRITICAL POINT No 2
....................
HEAT OF FORMATION = -35.291044 KCAL
RMS GRADIENT NORM = 0.007649 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = D2 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.52088 1
3 C 1.52088 112.21398 * 2 1
4 C 1.52088 111.55770 * -29.93933 * 3 2 1
5 C 1.52088 111.55517 * -30.14209 * 1 2 3
6 C 1.52088 111.56772 * 62.75057 * 5 1 2
7 H 1.12120 109.54732 * 90.59606 * 1 2 3
8 H 1.12120 109.61370 * -151.71722 * 1 2 3
9 H 1.12120 109.70654 * 121.28183 * 2 3 1
10 H 1.12120 108.98228 * -121.70482 * 2 3 1
11 H 1.12120 109.54343 * 90.80051 * 3 2 1
12 H 1.12120 109.61328 * -151.51398 * 3 2 1
13 H 1.12120 109.52404 * 184.55557 * 4 3 2
14 H 1.12120 108.88890 * -58.29523 * 4 3 2
15 H 1.12120 106.59192 * 51.24563 * 5 4 3
16 H 1.12120 137.68108 * -166.34359 * 5 4 3
17 H 1.12120 109.63636 * 121.38673 * 6 5 4
18 H 1.12120 108.89553 * -121.78879 * 6 5 4
CRITICAL POINT No 3
....................
HEAT OF FORMATION = 68.531095 KCAL
RMS GRADIENT NORM = 0.015153 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = C1 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 C 1.52088 1
3 C 1.52088 112.13620 * 2 1
4 C 1.52088 116.14403 * -91.58729 * 3 2 1
5 C 1.52088 111.50348 * -49.76363 * 1 2 3
6 C 1.52088 109.78808 * 50.54448 * 5 1 2
7 H 1.12120 109.47058 * -171.36756 * 1 2 3
8 H 1.12120 109.09486 * 70.94698 * 1 2 3
9 H 1.12120 109.28289 * 121.45883 * 2 3 1
10 H 1.12120 108.73584 * -121.01989 * 2 3 1
11 H 1.12120 103.63365 * 24.07010 * 3 2 1
12 H 1.12120 115.25638 * 131.78058 * 3 2 1
13 H 1.12120 119.55342 * 23.86167 * 4 3 2
14 H 1.12120 119.25747 * -164.33722 * 4 3 2
15 H 1.12120 122.15844 * -0.07077 * 5 4 3
16 H 1.12120 130.05307 * 177.26562 * 5 4 3
17 H 1.12120 113.87926 * 221.26848 * 6 5 4
18 H 1.12120 113.57800 * 91.43235 * 6 5 4
ELAPSED TIME IN QUENCHING 21.53 SECONDS
CALLS TO COST FNCT IN QUENCHING: 1633
ENLARGED CLUSTERING ANALYSIS OF CRITICAL POINTS
-----------------------------------------------
TABLE OF NEARLY IDENTICAL CONFIGURATIONS AT THRESHOLD = 1.10 A 
ENERGY ,CONFIGURATIONS (A "*" MEANS IDENTICAL)
2
-38.4617 1*
-35.2910 2.*
68.5311 3..*
NUMBER OF CONFIGURATIONS KEPT: 3
ELAPSED WALL CLOCK TIME : 12.62 SECONDS
FULL COMPUTATION TIME : 47.30 SECONDS
|
This section lists the dedicated annealing keywords found by the program. |
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Information on the methods and criteria that annealing will use is listed in this section of the output. |
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This section lists the active penalty functions defined by the annealing keywords. |
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The lower bounds, beginning values, and upper bounds for the optimizable parameters are summarized in this table. The user should carefully examine this table to ensure that the proper limits have been defined. |
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For PEN2 or PEN2GRP, a table of located bonded atoms are noted here. This information details which bonds will be enforced during the course of the simulated annealing. |
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These are the coordinates at the end of the annealing configuration search. |
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This table describes the presorted configurations and eliminates identical members from consideration. In this case, the four final candidates are revealed as non-identical and so none are filtered out. The threshold for filtering is controlled by FILTER (default=1.0) and occurs after each major phase of simulated annealing. A smaller value of FILTER can be used to minimize the chance of missing a minima, but this noticeably increases the amount of time required in the quenching process. |
The following molecule (methyl-N-methyl-amide) has been selected for illustration of the annealing procedure in the case of a relatively rigid system:
As mentioned in the section called “Strategies for Annealing Searches”, the general strategy to use is to divide the conformational search problem into primary and secondary degrees of freedom. Then a connectivity may be defined which allows an explicit description of the primary degrees of freedom. In this case, three primary degrees of freedom may be identified as the rotation about bonds C1-N3A, C4-N3B, and C5-C1C. The following is a viable (but not necessarily unique) connectivity pattern for this system that produces explicit descriptions of the primary degrees of freedom. (Note that the superscripts A, B, and C above identify below which of the dihedrals are used to specify the rotations.)
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 O 1.243077 1 0.000000 0 0.000000 0 1 0 0 N 1.366966 1 121.946787 1 0.000000 0 1 2 0 C 1.520000 1 120.615770 1 -0.000067A 1 3 1 2 C 1.540000 1 123.093733 1 -179.998834 1 1 2 3 H 0.986177 1 121.170189 1 179.991444 1 3 1 4 H 1.004440 1 108.958790 1 0.000000B 1 4 3 1 H 1.004440 1 108.958790 1 120.000000 1 4 3 7 H 1.000000 1 109.885165 1 -120.000000 1 4 3 7 H 1.004440 1 108.958790 1 180.000000C 1 5 1 2 H 1.004440 1 108.958790 1 120.000000 1 5 1 10 H 1.000000 1 109.885165 1 -120.000000 1 5 1 10
As mentioned in the section called “Geometry Specification”, this modular designation of the hydrogen atoms of a methyl group allows easy manipulation of the orientation of the entire group by altering one dihedral angle. In this example, the master degrees of freedom are defined by the dihedrals of particular atoms: the dihedral on H7for the C4 methyl (C4-N3 rotation), the dihedral on H10 for the C5 methyl (C5-C1 rotation), and the dihedral on C5 for the C1-N3 rotation. The LIMIT keyword can now be used to define boundaries for the search of conformational space. The secondary variables are not important to the annealing procedure and should be limited to about 10% of their original value. (Note that all annealing boundary conditions are ignored during the local quenching of the located minima.) The definition of the problem in these terms requires some chemical knowledge and intuition, but saves enormous computational effort. The final input and results files for the problem is listed below.
am1 rhf singlet t=auto anneal truste filter=1.2 noxyz limit
|
The keyword ANNEAL activates
energy-based annealing. LIMIT is used
to restrict the range the over which the geometry can vary. The FILTER= |
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The dihedrals on these lines comprise the three primary degrees of freedom. |
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This is the extra input section marker for reaction path data. Note, that this marker can be shortened to “$$ limit”. Details of these markers are found in the section called “Extra Input Data”. |
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These are the lower limits each geometric parameter can assume. Note that most are very close to their initial values but items # 6, 15, and 24 have a lower limit of -180.00. |
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These are the upper limits each geometric parameter can assume. As before, most are very close to their initial values but items # 6, 15, and 24 now have an upper limit of 180.00. The range -180 to +180 represent a full circle rotation about the required bonds. |
Timestamp: 2011-09-02-10-31-27-00000008B8-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Sep-02-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C3H7N1O1
methyl-n-methylamide
Annealing on rigid system: LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -47.273807 kcal
= -197.840883 kJ
ELECTRONIC ENERGY = -3372.707818 eV
CORE-CORE REPULSION = 2364.399293 eV
TOTAL ENERGY = -1008.308525 eV
GRADIENT NORM = 0.136535
RMS GRADIENT NORM = 0.024928
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 9.919350 eV
HOMO-LUMO GAP = 11.396568 eV
DIPOLE = 3.512983 debyes
MOLECULAR WEIGHT = 73.094400
MOLECULAR POINT GROUP = C1 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 27
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE FILTER=1.2 NOXYZ LIMIT
methyl-n-methylamide
Annealing on rigid system: LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.3005
O 1.247344 1 0.000000 0 0.000000 0 1 0 0 -0.3707
N 1.381133 1 121.226528 1 0.000000 0 1 2 0 -0.3919
C 1.426634 1 123.134683 1 0.930309 1 3 1 2 -0.0753
C 1.509608 1 121.506124 1 -179.607660 1 1 2 3 -0.2429
H 0.989975 1 119.083610 1 178.138046 1 3 1 4 0.2203
H 1.123743 1 110.042025 1 -123.258755 1 4 3 1 0.0657
H 1.123259 1 110.128295 1 120.142939 1 4 3 7 0.1180
H 1.123948 1 110.290251 1 -119.663478 1 4 3 7 0.0639
H 1.117269 1 108.671005 1 -2.926591 1 5 1 2 0.1176
H 1.116502 1 110.320733 1 119.387121 1 5 1 10 0.0986
H 1.116278 1 110.774936 1 -119.678593 1 5 1 10 0.0962
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-09-02-10-31-27-00000008B8-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Sep-02-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C3H7N1O1
methyl-n-methylamide
Annealing on rigid system: LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -47.128097 kcal
= -197.231086 kJ
ELECTRONIC ENERGY = -3381.382435 eV
CORE-CORE REPULSION = 2373.080228 eV
TOTAL ENERGY = -1008.302207 eV
GRADIENT NORM = 0.146199
RMS GRADIENT NORM = 0.026692
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 9.968793 eV
HOMO-LUMO GAP = 11.417545 eV
DIPOLE = 3.812818 debyes
MOLECULAR WEIGHT = 73.094400
MOLECULAR POINT GROUP = C1 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 27
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE FILTER=1.2 NOXYZ LIMIT
methyl-n-methylamide
Annealing on rigid system: LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.2989
O 1.247945 1 0.000000 0 0.000000 0 1 0 0 -0.3723
N 1.382533 1 118.914981 1 0.000000 0 1 2 0 -0.3914
C 1.424011 1 123.339115 1 -174.380801 1 3 1 2 -0.0691
C 1.505834 1 121.890796 1 178.881179 1 1 2 3 -0.2367
H 0.993653 1 117.637889 1 170.185844 1 3 1 4 0.2332
H 1.123800 1 110.478541 1 -49.571301 1 4 3 1 0.0761
H 1.125295 1 111.400134 1 120.222450 1 4 3 7 0.0618
H 1.122051 1 109.493726 1 -119.678278 1 4 3 7 0.0858
H 1.117092 1 108.802145 1 6.064562 1 5 1 2 0.1159
H 1.116714 1 110.731439 1 120.021331 1 5 1 10 0.0962
H 1.117107 1 110.071756 1 -119.390425 1 5 1 10 0.1015
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
Timestamp: 2011-09-02-10-31-27-00000008B8-win64
User Info: John Millam, Nahum,
SUMMARY OF AM1 CALCULATION
Sep-02-2011
AMPAC Version 10.0.1
Presented by:
Semichem, Inc.
www.semichem.com
FORMULA: C3H7N1O1
methyl-n-methylamide
Annealing on rigid system: LIMIT
GEOMETRY NORMALLY RETURNED BY SIMULATED ANNEALING
SCF FIELD WAS ACHIEVED
FINAL HEAT OF FORMATION = -46.479573 kcal
= -194.517012 kJ
ELECTRONIC ENERGY = -3377.189894 eV
CORE-CORE REPULSION = 2368.915810 eV
TOTAL ENERGY = -1008.274084 eV
GRADIENT NORM = 0.118537
RMS GRADIENT NORM = 0.021642
UNSTABLE MODE(S) = 0 ( ESTIMATE )
IONIZATION POTENTIAL = 9.953249 eV
HOMO-LUMO GAP = 11.428904 eV
DIPOLE = 3.756254 debyes
MOLECULAR WEIGHT = 73.094400
MOLECULAR POINT GROUP = Cs 0.100000
NO. OF FILLED LEVELS = 15 (OCC = 2)
TOTAL NUMBER OF ORBITALS = 27
FINAL GEOMETRY OBTAINED CHARGE
AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE FILTER=1.2 NOXYZ LIMIT
methyl-n-methylamide
Annealing on rigid system: LIMIT
C 0.000000 0 0.000000 0 0.000000 0 0 0 0 0.3009
O 1.249438 1 0.000000 0 0.000000 0 1 0 0 -0.3786
N 1.380579 1 118.294584 1 0.000000 0 1 2 0 -0.3920
C 1.423729 1 124.574106 1 179.249337 1 3 1 2 -0.0666
C 1.505574 1 120.930373 1 -179.925618 1 1 2 3 -0.2349
H 0.994000 1 117.229073 1 -178.915734 1 3 1 4 0.2338
H 1.124457 1 111.091737 1 -59.426313 1 4 3 1 0.0687
H 1.124450 1 111.024190 1 120.524265 1 4 3 7 0.0692
H 1.122134 1 109.428362 1 -119.763167 1 4 3 7 0.0857
H 1.117948 1 108.228375 1 57.897759 1 5 1 2 0.1125
H 1.114605 1 113.737957 1 121.236172 1 5 1 10 0.0891
H 1.117909 1 108.238855 1 -117.462003 1 5 1 10 0.1121
0 0.000000 0 0.000000 0 0.000000 0 0 0 0
|
This is the data relating to the first minimum located by annealing, and is a refined version of the input structure pictured in Figure 30.2, “Trans-minimum”. This structure happens to be the global minimum on the PES and is referred to as the “trans-minimum.” |
|
This is the data relating to the second minimum located by annealing. It is referred to as the “cis-minimum” (Figure 30.3, “Cis-minimum”). |
Timestamp: 2011-09-02-10-31-27-00000008B8-win64
User Info: John Millam, Nahum,
*******************************************************************************
AM1 CALCULATION RESULTS
*******************************************************************************
* AMPAC Version 10.0.1
* Presented by:
*
* Semichem, Inc.
* www.semichem.com
*
* AM1 - THE AM1 HAMILTONIAN TO BE USED
* RHF - RESTRICTED HARTREE-FOCK CALCULATION
* ANNE - SIMULATED ANNEALING ON ENERGY ONLY
* TRUSTE - MINIMIZE ENERGY USING TRUST REGION METHOD
* NOXYZ - CARTESIAN COORDINATES NOT TO BE PRINTED
* T=AUTO - AUTOMATIC DETERMINATION OF ALLOWED TIME
* SINGLET - IS THE REQUIRED SPIN MULTIPLICITY
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AM1 RHF SINGLET T=AUTO ANNEAL TRUSTE FILTER=1.2 NOXYZ LIMIT
methyl-n-methylamide
Annealing on rigid system: LIMIT
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 O 1.24308 * 1
3 N 1.36697 * 121.94679 * 1 2
4 C 1.52000 * 120.61577 * 0.00000 * 3 1 2
5 C 1.54000 * 123.09373 * -179.99000 * 1 2 3
6 H 0.98618 * 121.17019 * 179.99000 * 3 1 4
7 H 1.00444 * 108.95879 * -60.00000 * 4 3 1
8 H 1.00444 * 108.95879 * 120.00000 * 4 3 7
9 H 1.00000 * 109.88517 * -120.00000 * 4 3 7
10 H 1.00444 * 108.95879 * 120.00000 * 5 1 2
11 H 1.00444 * 108.95879 * 120.00000 * 5 1 10
12 H 1.00000 * 109.88517 * -120.00000 * 5 1 10
MOLECULAR POINT GROUP SYMMETRY CRITERIA
Cs 0.10000000
SINGLET STATE CALCULATION
RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15
** REFERENCES TO PARAMETERS **
H (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
C (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
N (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
O (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
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* KEYWORDS DEDICATED TO SIMULATED ANNEALING SECTION
*
* LIMIT - EXPLICIT PERIODIC CONDITIONS GIVEN
* FILTER= - SET THRESHOLD OF DISTINGUISHED CONFIGURATION TO 1.200
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STANDARD DEVIATION ON ENERGY (KCAL) 0.00000055521
STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD) 0.00009841 0.00018732 0.00013159
SIMULATED ANNEALING BY METROPOLIS SCHEME IN 30 VARIABLES
VERSION 2.0 (MAY 2000)
THERMALIZATION THRESHOLD ON COST FNCT 0.080
MAXIMUM STEP SIZE 2.00000
CONVERGENCE CRITERION ON STEP SIZE 0.06325
MAXIMUM NUMBER OF STEPS AT EACH TEMPERATURE 1000
FIRST TEMPERATURE (HOT) SET TO 50.00
TEMPERATURE EXPONENTIAL DECAY 0.80
LAST TEMPERATURE (COLD) SET TO 0.50
RANDOM SEQUENCE INITIATOR -9876566
MARKOV CHAIN STUDIED BY PIECES OF 20
No OF TEMPERATURES TO DETECT A FROZEN SYSTEM 2
EQUIVALENCE THRESHOLD IN CLUSTERING ANALYSIS 1.20
BAND-PASS FILTER NO 1 CENTERED AT 1.40 ANGSTROMS
HALF BAND-WIDTH 13.50 %
CAN HOLD 250 CANDIDATES FOR QUENCHING.
PERIODIC BOUNDARY CONDITIONS (ANGSTROMS, DEGREES)
LOWER BOUND 1.2000 1.3000 110.0000 1.5000 110.0000 -180.0000
1.5000 100.0000 -190.0000 0.9000 100.0000 160.0000
0.9000 100.0000 -180.0000 0.9000 100.0000 100.0000
0.9000 100.0000 -140.0000 0.9000 100.0000 -180.0000
0.9000 100.0000 100.0000 0.9000 100.0000 -140.0000
TRIAL COORD 1.2431 1.3670 121.9468 1.5200 120.6158 0.0000
1.5400 123.0937 -179.9900 0.9862 121.1702 179.9900
1.0044 108.9588 -60.0000 1.0044 108.9588 120.0000
1.0000 109.8852 -120.0000 1.0044 108.9588 120.0000
1.0044 108.9588 120.0000 1.0000 109.8852 -120.0000
UPPER BOUND 1.3000 1.4000 130.0000 1.6000 130.0000 180.0000
1.6000 140.0000 -170.0000 1.1000 130.0000 200.0000
1.1000 130.0000 180.0000 1.1000 130.0000 140.0000
1.1000 130.0000 -100.0000 1.1000 130.0000 180.0000
1.1000 130.0000 140.0000 1.1000 130.0000 -100.0000
COST FNCT IS ENERGY (KCAL/MOLE)
VISIT OF THE PES BY SIMULATED ANNEALING
---------------------------------------
* * * SYSTEM LOOKS FROZEN AT TEMPERATURE 6.7109 KCAL
NORMAL END AFTER 1111 CALLS TO COST FNCT
ELAPSED TIME IN ANNEALING 10.11 SECONDS
CLUSTERING ANALYSIS OF CONFORMATIONS
------------------------------------
KEEP 5 CONFORMATIONS FROM 28 SELECTED AT PES VISIT
QUENCHING OF REMAINING CONFORMATIONS
------------------------------------
PERFORMED WITHOUT PERIODIC BOUNDARIES.
MINIMIZE ENERGY BY TRUST ALGORITHM
QUENCHING No 1 -- STAGE 1 OF 1 ( 0.08 SECONDS)
..................................................
HEAT OF FORMATION = -46.479573 KCAL
RMS GRADIENT NORM = 0.021643 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
1.2494 1.3806 118.2946 1.4237 124.5741 -180.7507 1.5056 120.9304
-179.9256 0.9940 117.2291 181.0843 1.1245 111.0917 -59.4263 1.1244
111.0242 120.5243 1.1221 109.4284 -119.7632 1.1179 108.2284 57.8978
1.1146 113.7380 121.2362 1.1179 108.2389 -117.4620
QUENCHING No 2 -- STAGE 1 OF 1 ( 0.14 SECONDS)
..................................................
HEAT OF FORMATION = -47.273807 KCAL
RMS GRADIENT NORM = 0.024924 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
1.2473 1.3811 121.2265 1.4266 123.1347 0.9303 1.5096 121.5061
-179.6077 0.9900 119.0836 178.1380 1.1237 110.0420 -123.2588 1.1233
110.1283 120.1429 1.1239 110.2903 -119.6635 1.1173 108.6710 -2.9266
1.1165 110.3207 119.3871 1.1163 110.7749 -119.6786
QUENCHING No 3 -- STAGE 1 OF 1 ( 0.12 SECONDS)
..................................................
HEAT OF FORMATION = -47.128097 KCAL
RMS GRADIENT NORM = 0.026692 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
CURRENT COORDINATES (ANGSTROMS, DEGREES)
1.2479 1.3825 118.9150 1.4240 123.3391 -174.3808 1.5058 121.8908
-181.1188 0.9937 117.6379 170.1858 1.1238 110.4785 -49.5713 1.1253
111.4001 120.2225 1.1221 109.4937 -119.6783 1.1171 108.8021 6.0646
1.1167 110.7314 120.0213 1.1171 110.0718 -119.3904
QUENCHING No 4 -- STAGE 1 OF 1 ( 0.06 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
QUENCHING No 5 -- STAGE 1 OF 1 ( 0.11 SECONDS)
..................................................
* * * QUENCHING INTERRUPTED: POINT PREVIOUSLY FOUND.
TIME CONSUMPTION OF STAGE 1: 0.58 SECONDS
ON 3 POINTS AT END OF STAGE 1, 3 FULFILL STATIONARITY AND ENERGETIC REQUESTS.
DETAILS ON NON EQUIVALENT CRITICAL POINTS FOUND (ENERGY SORTED)
---------------------------------------------------------------
CRITICAL POINT No 1
....................
HEAT OF FORMATION = -47.273807 KCAL
RMS GRADIENT NORM = 0.024924 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = C1 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 O 1.24734 * 1
3 N 1.38113 * 121.22653 * 1 2
4 C 1.42663 * 123.13468 * 0.93031 * 3 1 2
5 C 1.50961 * 121.50612 * -179.60766 * 1 2 3
6 H 0.98998 * 119.08361 * 178.13805 * 3 1 4
7 H 1.12374 * 110.04202 * -123.25875 * 4 3 1
8 H 1.12326 * 110.12829 * 120.14294 * 4 3 7
9 H 1.12395 * 110.29025 * -119.66348 * 4 3 7
10 H 1.11727 * 108.67101 * -2.92659 * 5 1 2
11 H 1.11650 * 110.32073 * 119.38712 * 5 1 10
12 H 1.11628 * 110.77494 * -119.67859 * 5 1 10
CRITICAL POINT No 2
....................
HEAT OF FORMATION = -47.128097 KCAL
RMS GRADIENT NORM = 0.026692 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = C1 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 O 1.24794 * 1
3 N 1.38253 * 118.91498 * 1 2
4 C 1.42401 * 123.33912 * -174.38080 * 3 1 2
5 C 1.50583 * 121.89080 * -181.11882 * 1 2 3
6 H 0.99365 * 117.63789 * 170.18584 * 3 1 4
7 H 1.12380 * 110.47854 * -49.57130 * 4 3 1
8 H 1.12529 * 111.40013 * 120.22245 * 4 3 7
9 H 1.12205 * 109.49373 * -119.67828 * 4 3 7
10 H 1.11709 * 108.80215 * 6.06456 * 5 1 2
11 H 1.11671 * 110.73144 * 120.02133 * 5 1 10
12 H 1.11711 * 110.07176 * -119.39042 * 5 1 10
CRITICAL POINT No 3
....................
HEAT OF FORMATION = -46.479573 KCAL
RMS GRADIENT NORM = 0.021643 KCAL/ANGSTROMS
CRITICAL POINT INDEX = 0 ESTIMATE
MOLECULAR POINT GROUP = Cs 0.100000
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C
2 O 1.24944 * 1
3 N 1.38058 * 118.29458 * 1 2
4 C 1.42373 * 124.57411 * -180.75066 * 3 1 2
5 C 1.50557 * 120.93037 * -179.92562 * 1 2 3
6 H 0.99400 * 117.22907 * 181.08427 * 3 1 4
7 H 1.12446 * 111.09174 * -59.42631 * 4 3 1
8 H 1.12445 * 111.02419 * 120.52427 * 4 3 7
9 H 1.12213 * 109.42836 * -119.76317 * 4 3 7
10 H 1.11795 * 108.22838 * 57.89776 * 5 1 2
11 H 1.11460 * 113.73796 * 121.23617 * 5 1 10
12 H 1.11791 * 108.23885 * -117.46200 * 5 1 10
ELAPSED TIME IN QUENCHING 0.66 SECONDS
CALLS TO COST FNCT IN QUENCHING: 80
ENLARGED CLUSTERING ANALYSIS OF CRITICAL POINTS
-----------------------------------------------
TABLE OF NEARLY IDENTICAL CONFIGURATIONS AT THRESHOLD = 1.32 A
ENERGY ,CONFIGURATIONS (A "*" MEANS IDENTICAL)
2
-47.2738 1*
-47.1281 2.*
-46.4796 3..*
NUMBER OF CONFIGURATIONS KEPT: 3
ELAPSED WALL CLOCK TIME : 20.11 SECONDS
FULL COMPUTATION TIME : 12.82 SECONDS
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These are the upper and lower boundaries along with the initial values for each coordinate. |
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These are the coordinates at the end of the annealing quenching phase. |
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This is the trans-minimum geometry. |
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This is the cis-minimum geometry. |
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This table describes the presorted configurations and eliminates identical members from consideration. The threshold for filtering is controlled by FILTER (default=1.0) and occurs after each major phase of simulated annealing. A smaller value of FILTER can be used to minimize the chance of missing a minimum, but this noticeably increases the amount of time required in the quenching process. |
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Copyright © 1992-2013 Semichem, Inc. All rights reserved. |
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| Chapter 29. Intrinsic Reaction Coordinate (IRC) Calculation |  |
Chapter 31. Electrostatic Potential Charges (ESP) |