
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> Number of atoms (or variables)  determined as     79
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     8
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp31.ch.
                 Created on  5/28/12 at 12: 3:15 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  237 Cartesian coordinates will be optimised for   79 CHARMM atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -292.6263491     RMS force=    0.9431159686E-06
 OPTIM> Final energy  =    -287.7827927     RMS force=    0.8595389977E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     11404.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.51     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      77.61587555    
 Double-ended search iterations= 484 RMS= 32.2779 Dev= 4.32% S= 23.62 time= 1.66
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   1.03

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     542 steps. Energy=    -288.4878398       time=       0.43
 Minus side of path:                     551 steps. Energy=    -287.3361483       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.4878398  2.5305         -285.9573026  1.3788         -287.3361483   9.138   8.485   2.644  29.882
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     5959.7    
 decide> The unconnected minima in the chain and their distances are:
     2        7.91     4     3       17.61     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.6430 Dev= 0.56% S= 8.33 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   0.64

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     539 steps. Energy=    -287.7827927       time=       0.43
 Minus side of path:                     534 steps. Energy=    -287.3361483       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7827927  1.9047         -285.8780944  1.4581         -287.3361483   9.734   7.910   4.005  19.727
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 177 RMS= 17.2216 Dev= 34.07% S= 30.75 time= 0.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.81

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     531 steps. Energy=    -285.5555643       time=       0.42
 Minus side of path:                     518 steps. Energy=    -288.4878398       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -285.5555643  3.1167         -282.4388964  6.0489         -288.4878398   4.932   3.693  26.768   2.951
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     6665.4    
 decide> The unconnected minima in the chain and their distances are:
     5       18.82     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      55.16015368    
 Double-ended search iterations= 239 RMS= 19.1510 Dev= 16.34% S= 30.44 time= 0.69
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        124
 DNEB run yielded 1 true transition state(s) time=   1.97

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     494 steps. Energy=    -287.7588860       time=       0.39
 Minus side of path:                     523 steps. Energy=    -289.6669078       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7588860 0.31786E-01     -287.7271000  1.9398         -289.6669078   8.345   8.167   2.419  32.663
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     3902.6    
 decide> The unconnected minima in the chain and their distances are:
     3        9.72     7     6       14.40     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 73 RMS= 20.0902 Dev= 35.34% S= 44.88 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   0.91

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     561 steps. Energy=    -288.7577410       time=       0.46
 Minus side of path:                     535 steps. Energy=    -289.6669078       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7577410  2.8038         -285.9538943  3.7130         -289.6669078   9.043   4.324   7.189  10.989
        *NEW* (Placed in 8)                                     Known (#7)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 140 RMS= 0.4767 Dev= 0.47% S= 15.20 time= 0.32
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   1.67

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     486 steps. Energy=    -287.7588860       time=       0.39
 Minus side of path:                     638 steps. Energy=    -290.1937507       time=       0.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7588860 0.74473E-02     -287.7514387  2.4423         -290.1937507  11.610  11.227   4.908  16.097
        Known (#6)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     2071.5    
 decide> The unconnected minima in the chain and their distances are:
     3       10.25     8     9        9.98     1 
 

 tryconnect> 105-iteration DNEB run for minima 3_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 119 RMS= 16.0908 Dev= 21.96% S= 39.87 time= 0.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   1.00

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     517 steps. Energy=    -287.9953244       time=       0.42
 Minus side of path:                     521 steps. Energy=    -288.7577410       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.9953244 0.96498E-01     -287.8988266 0.85891         -288.7577410   4.793   4.729   2.837  27.846
        *NEW* (Placed in 10)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.3894 Dev= 0.45% S= 10.15 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   0.62

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     572 steps. Energy=    -291.7661692       time=       0.49
 Minus side of path:                     480 steps. Energy=    -290.1937507       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.7661692  2.0080         -289.7581700 0.43558         -290.1937507   9.932   9.379   5.750  13.740
        *NEW* (Placed in 11)                                    Known (#9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     1415.7    
 decide> The unconnected minima in the chain and their distances are:
     5       10.93     8    11        4.81     1 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 118 RMS= 22.7365 Dev= 40.12% S= 49.44 time= 0.20
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   1.15

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     565 steps. Energy=    -287.2005961       time=       0.48
 Minus side of path:                     562 steps. Energy=    -287.7588860       time=       0.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.2005961  2.0820         -285.1186305  2.6403         -287.7588860  14.385  13.250   4.276  18.475
        *NEW* (Placed in 12)                                    Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.1363 Dev= 0.33% S= 4.92 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   0.60

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     497 steps. Energy=    -291.7661692       time=       0.41
 Minus side of path:                     503 steps. Energy=    -292.6263491       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.7661692 0.62496         -291.1412103  1.4851         -292.6263491   5.601   4.813   9.684   8.158
        Known (#11)                                             Known (#1)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1347.8    
 decide> The unconnected minima in the chain and their distances are:
     2       11.05     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 220 RMS= 34.0492 Dev= 2.23% S= 74.64 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   1.30
 isnewts> transition state is the same as number        9 energy=     -285.1186304620
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 11 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     578 steps. Energy=    -287.7588860       time=       0.49
 Minus side of path:                     592 steps. Energy=    -287.2005961       time=       0.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7588860  2.6403         -285.1186305  2.0820         -287.2005961  14.383  13.251   4.283  18.445
        Known (#6)                                              Known (#12)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     1398.6    
 decide> The unconnected minima in the chain and their distances are:
     5       11.18     7 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 7_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 125 RMS= 17.3944 Dev= 21.41% S= 49.14 time= 0.21
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.81

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     527 steps. Energy=    -287.7588860       time=       0.43
 Minus side of path:                     538 steps. Energy=    -288.9255964       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7588860  2.6815         -285.0773660  3.8482         -288.9255964   4.020   3.638  21.324   3.705
        Known (#6)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 13 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1565.2    
 decide> The unconnected minima in the chain and their distances are:
     2       11.61     8 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 474 RMS= 20.2313 Dev= 1.54% S= 11.97 time= 0.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   1.01

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     521 steps. Energy=    -287.7827927       time=       0.41
 Minus side of path:                     507 steps. Energy=    -289.7024681       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -287.7827927 0.86550         -286.9172882  2.7852         -289.7024681   8.875   7.770   3.174  24.890
        Known (#2)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 14 minima and 13 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     420.04    
 decide> The unconnected minima in the chain and their distances are:
    14        7.49     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 14_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 16.8841 Dev= 35.19% S= 38.46 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   1.06
 isnewts> transition state is the same as number        5 energy=     -285.9538942892
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 14 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     553 steps. Energy=    -288.7577410       time=       0.45
 Minus side of path:                     540 steps. Energy=    -289.6669078       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7577410  2.8038         -285.9538943  3.7130         -289.6669078   9.043   4.323   7.213  10.952
        Known (#8)                                              Known (#7)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 14 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     622.44    
 decide> The unconnected minima in the chain and their distances are:
    14        8.54     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 14_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 113 RMS= 16.9741 Dev= 65.91% S= 13.86 time= 0.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        177
 DNEB run yielded 1 true transition state(s) time=   3.46

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     566 steps. Energy=    -290.3557722       time=       0.46
 Minus side of path:                     531 steps. Energy=    -291.2173895       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.3557722  4.9178         -285.4379696  5.7794         -291.2173895  17.628  14.941   5.564  14.199
        *NEW* (Placed in 15)                                    *NEW* (Placed in 16)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 16 minima and 15 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     840.08    
 decide> The unconnected minima in the chain and their distances are:
    14        7.49     7 
 

 tryconnect> 595-iteration DNEB run for minima 7_S and 14_F using 17 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      60.81406943    
 Double-ended search iterations= 595 RMS= 0.2571 Dev= 0.38% S= 9.72 time= 5.59
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   0.72

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     541 steps. Energy=    -288.7434456       time=       0.44
 Minus side of path:                     520 steps. Energy=    -289.7024681       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7434456  2.8612         -285.8822092  3.8203         -289.7024681   8.633   4.266   7.621  10.366
        *NEW* (Placed in 17)                                    Known (#14)
 Unconnected minimum 17 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 17 minima and 16 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     428.44    
 decide> The unconnected minima in the chain and their distances are:
    17        7.54     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 17_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 90 RMS= 15.0670 Dev= 38.95% S= 22.85 time= 0.10
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     529 steps. Energy=    -288.7577410       time=       0.42
 Minus side of path:                     499 steps. Energy=    -288.7434456       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -288.7577410 0.29196         -288.4657797 0.27767         -288.7434456   6.099   5.823   7.685  10.279
        *NEW* (Placed in 18)                                    Known (#17)
 Unconnected minimum 18 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 18 minima and 17 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     110.21    
 decide> The unconnected minima in the chain and their distances are:
    18        4.79     8 
 

 checkpair> Energies of the minima in the pair     8   18 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 8_S and 18_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.3198 Dev= 0.61% S= 7.20 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   0.66

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                     531 steps. Energy=    -289.6669078       time=       0.43
 Minus side of path:                     534 steps. Energy=    -288.7577410       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.6669078  4.0552         -285.6117308  3.1460         -288.7577410   8.298   4.325   7.529  10.492
        *NEW* (Placed in 19)                                    Known (#18)
 Unconnected minimum 19 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 15 >>>>>>>>>>>>>>>>>>>>> 19 minima and 18 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     110.17    
 decide> The unconnected minima in the chain and their distances are:
    19        4.79     7 
 

 checkpair> Energies of the minima in the pair     7   19 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 7_S and 19_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.6135 Dev= 0.31% S= 7.19 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   0.71
 isnewts> transition state is the same as number        5 energy=     -285.9538942892
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 16 >>>>>>>>>>>>>>>>>>>>> 19 minima and 18 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     180.04    
 decide> The unconnected minima in the chain and their distances are:
    18        5.65     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 18_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.3487 Dev= 0.78% S= 6.44 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   0.59

 >>>>>  Path run for ts 19 ...
 Plus  side of path:                     539 steps. Energy=    -289.6669078       time=       0.44
 Minus side of path:                     518 steps. Energy=    -288.7577410       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -289.6669078  2.9679         -286.6990487  2.0587         -288.7577410   7.300   5.649  13.878   5.692
        Known (#7)                                              Known (#18)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -292.6263491  1.4851        -291.1412103 0.62496        -291.7661692   5.601   4.813   9.684   8.158
   8     -291.7661692  2.0080        -289.7581700 0.43558        -290.1937507   9.932   9.379   5.750  13.740
   6     -290.1937507  2.4423        -287.7514387 0.74473E-02    -287.7588860  11.610  11.227   4.908  16.097
   4     -287.7588860 0.31786E-01    -287.7271000  1.9398        -289.6669078   8.345   8.167   2.419  32.663
  19     -289.6669078  2.9679        -286.6990487  2.0587        -288.7577410   7.300   5.649  13.878   5.692
  17     -288.7577410 0.29196        -288.4657797 0.27767        -288.7434456   6.099   5.823   7.685  10.279
  16     -288.7434456  2.8612        -285.8822092  3.8203        -289.7024681   8.633   4.266   7.621  10.366
  13     -289.7024681  2.7852        -286.9172882 0.86550        -287.7827927   8.875   7.770   3.174  24.890

 Number of TS in the path       =      8
 Number of cycles               =     16

 Elapsed time=                                50.90
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             53559 time=          28.29 %= 55.6
 OPTIM> # of energy+gradient+Hessian calls=      1034 time=           1.05 %=  2.1
