
 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)@comp34.ch.
                 Created on  5/28/12 at 11:52:22 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=    -294.3264600     RMS force=    0.7949688836E-06
 OPTIM> Final energy  =    -293.6315934     RMS force=    0.8710865399E-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=     2146.0    
 decide> The unconnected minima in the chain and their distances are:
     2       12.90     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4404 Dev= 0.72% S= 14.68 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   1.21

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     478 steps. Energy=    -292.6545945       time=       0.38
 Minus side of path:                     519 steps. Energy=    -294.5477649       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.6545945 0.46326         -292.1913334  2.3564         -294.5477649   6.192   4.486   9.451   8.359
        *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      2 steps with      2 missing connections, weight=     2253.5    
 decide> The unconnected minima in the chain and their distances are:
     2       11.97     3     3        8.14     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 3.6400 Dev= 0.34% S= 12.98 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   0.89

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     544 steps. Energy=    -292.5439228       time=       0.44
 Minus side of path:                     495 steps. Energy=    -292.4318497       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.5439228 0.68918         -291.8547424 0.57711         -292.4318497   8.771   6.039   3.170  24.918
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5765 Dev= 0.21% S= 8.92 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   0.88

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     484 steps. Energy=    -292.6545945       time=       0.42
 Minus side of path:                     477 steps. Energy=    -292.3066099       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.6545945 0.37511         -292.2794869 0.27123E-01     -292.3066099   2.842   2.720   2.583  30.580
        Known (#3)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     1479.6    
 decide> The unconnected minima in the chain and their distances are:
     2        8.62     6     6        6.43     3     7        8.31     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5135 Dev= 0.41% S= 9.19 time= 0.08
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=   4.43

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3234 Dev= 0.34% S= 6.76 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   0.88

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     484 steps. Energy=    -292.3066099       time=       0.38
 Minus side of path:                     466 steps. Energy=    -295.0702085       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.3066099 0.37625         -291.9303617  3.1398         -295.0702085   5.586   4.993   5.637  14.015
        Known (#7)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.1437 Dev= 0.32% S= 9.12 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   0.88
 isnewts> transition state is the same as number        3 energy=     -292.2794868615
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     466 steps. Energy=    -292.3066099       time=       0.37
 Minus side of path:                     483 steps. Energy=    -292.6545945       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.3066099 0.27123E-01     -292.2794869 0.37511         -292.6545945   2.842   2.720   2.583  30.585
        Known (#7)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     1578.3    
 decide> The unconnected minima in the chain and their distances are:
     2        8.86     5     5        9.59     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4258 Dev= 0.39% S= 9.53 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   1.61

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     483 steps. Energy=    -293.6315934       time=       0.38
 Minus side of path:                     557 steps. Energy=    -292.3742806       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.6315934  2.0291         -291.6024566 0.77182         -292.3742806  10.007   6.541   6.379  12.385
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4895 Dev= 0.36% S= 10.29 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   0.96
 isnewts> transition state is the same as number        1 energy=     -292.1913333652
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     522 steps. Energy=    -294.5477649       time=       0.42
 Minus side of path:                     478 steps. Energy=    -292.6545945       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.5477649  2.3564         -292.1913334 0.46326         -292.6545945   6.192   4.486   9.413   8.393
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1286.0    
 decide> The unconnected minima in the chain and their distances are:
     9       10.87     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.6716 Dev= 1.14% S= 12.14 time= 0.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     462 steps. Energy=    -297.7838886       time=       0.36
 Minus side of path:                     609 steps. Energy=    -298.0373891       time=       0.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.7838886  3.7691         -294.0147623  4.0226         -298.0373891   6.620   5.801   5.694  13.874
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     1480.8    
 decide> The unconnected minima in the chain and their distances are:
     9        8.23     5     6        5.47     8     4        9.12     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2964 Dev= 0.23% S= 8.55 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.78

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     506 steps. Energy=    -293.1602526       time=       0.40
 Minus side of path:                     474 steps. Energy=    -292.3742806       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.1602526 0.96875         -292.1915058 0.18277         -292.3742806   3.851   3.464   7.609  10.383
        *NEW* (Placed in 12)                                    Known (#9)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1670 Dev= 0.25% S= 5.58 time= 0.08
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   0.64

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     478 steps. Energy=    -295.0702085       time=       0.37
 Minus side of path:                     443 steps. Energy=    -292.4318497       time=       0.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.0702085  2.6404         -292.4298471 0.20026E-02     -292.4318497   5.565   5.473   3.375  23.408
        Known (#8)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8079 Dev= 0.23% S= 9.86 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   0.79
 isnewts> transition state is the same as number        1 energy=     -292.1913333652
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     995.49    
 decide> The unconnected minima in the chain and their distances are:
    12        9.98     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 12_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 3.1560 Dev= 0.52% S= 10.76 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   1.37
 isnewts> transition state is the same as number        1 energy=     -292.1913333652
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1265.7    
 decide> The unconnected minima in the chain and their distances are:
    12        6.43     5     6       10.00     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 12_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.5822 Dev= 0.17% S= 6.74 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   0.78

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     507 steps. Energy=    -292.5439228       time=       0.40
 Minus side of path:                     498 steps. Energy=    -293.1260029       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.5439228 0.62787         -291.9160509  1.2100         -293.1260029   7.407   6.056  10.256   7.703
        Known (#5)                                              *NEW* (Placed in 13)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5982 Dev= 0.64% S= 10.75 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   0.59

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     532 steps. Energy=    -294.3264600       time=       0.44
 Minus side of path:                     515 steps. Energy=    -292.2003199       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.3264600  6.0785         -288.2479163  3.9524         -292.2003199   9.294   6.311   7.630  10.354
        Known (#1)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 14 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     84.376    
 decide> The unconnected minima in the chain and their distances are:
    12        1.85    13     7        4.27    14 
 

 tryconnect> 70-iteration DNEB run for minima 12_F and 13_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0250 Dev= 0.13% S= 1.87 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   0.46

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     461 steps. Energy=    -293.1260029       time=       0.36
 Minus side of path:                     480 steps. Energy=    -293.1602526       time=       0.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.1260029 0.15406E-01     -293.1105971 0.49656E-01     -293.1602526   1.916   1.849  18.585   4.251
        Known (#13)                                             Known (#12)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_F and 14_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5930 Dev= 0.60% S= 4.88 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.69
 isnewts> transition state is the same as number        4 energy=     -291.9303617213
 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:                     484 steps. Energy=    -292.3066099       time=       0.42
 Minus side of path:                     481 steps. Energy=    -295.0702085       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.3066099 0.37625         -291.9303617  3.1398         -295.0702085   5.586   4.993   5.631  14.029
        Known (#7)                                              Known (#8)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 14 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     122.76    
 decide> The unconnected minima in the chain and their distances are:
     3        4.97    14 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 14_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7154 Dev= 0.69% S= 5.63 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   0.80
 isnewts> transition state is the same as number        3 energy=     -292.2794868615
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 14 minima and 14 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     156.10    
 decide> The unconnected minima in the chain and their distances are:
     7        4.27    14 
 

 tryconnect> 315-iteration DNEB run for minima 7_F and 14_S using 9 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 315 RMS= 1.4112 Dev= 5.36% S= 7.41 time= 1.62
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.58

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                     490 steps. Energy=    -295.2519585       time=       0.39
 Minus side of path:                     498 steps. Energy=    -293.4939233       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.2519585  5.2620         -289.9899501  3.5040         -293.4939233   7.057   6.444   4.489  17.599
        *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     10 steps with      2 missing connections, weight=     123.71    
 decide> The unconnected minima in the chain and their distances are:
     8        2.63    15    16        4.73    14 
 

 tryconnect> 70-iteration DNEB run for minima 8_F and 15_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0748 Dev= 0.07% S= 2.66 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   0.46

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                     436 steps. Energy=    -295.2519585       time=       0.33
 Minus side of path:                     445 steps. Energy=    -295.0702085       time=       0.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.2519585 0.25831         -294.9936455 0.76563E-01     -295.0702085   2.737   2.626  12.616   6.262
        Known (#15)                                             Known (#8)
 Unconnected minimum 15 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 14_S and 16_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1867 Dev= 0.33% S= 4.89 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=   0.58

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                     499 steps. Energy=    -292.2003199       time=       0.40
 Minus side of path:                     477 steps. Energy=    -293.4939233       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.2003199  1.3705         -290.8297737  2.6641         -293.4939233   5.916   4.727   7.038  11.224
        Known (#14)                                             Known (#16)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -294.3264600  6.0785        -288.2479163  3.9524        -292.2003199   9.294   6.311   7.630  10.354
  17     -292.2003199  1.3705        -290.8297737  2.6641        -293.4939233   5.916   4.727   7.038  11.224
  15     -293.4939233  3.5040        -289.9899501  5.2620        -295.2519585   7.057   6.444   4.489  17.599
  16     -295.2519585 0.25831        -294.9936455 0.76563E-01    -295.0702085   2.737   2.626  12.616   6.262
  10     -295.0702085  2.6404        -292.4298471 0.20026E-02    -292.4318497   5.565   5.473   3.375  23.408
   2     -292.4318497 0.57711        -291.8547424 0.68918        -292.5439228   8.771   6.039   3.170  24.918
  11     -292.5439228 0.62787        -291.9160509  1.2100        -293.1260029   7.407   6.056  10.256   7.703
  13     -293.1260029 0.15406E-01    -293.1105971 0.49656E-01    -293.1602526   1.916   1.849  18.585   4.251
   9     -293.1602526 0.96875        -292.1915058 0.18277        -292.3742806   3.851   3.464   7.609  10.383
   6     -292.3742806 0.77182        -291.6024566  2.0291        -293.6315934  10.007   6.541   6.379  12.385

 Number of TS in the path       =     10
 Number of cycles               =     12

 Elapsed time=                                39.01
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             35098 time=          18.48 %= 47.4
 OPTIM> # of energy+gradient+Hessian calls=      1033 time=           1.14 %=  2.9
