
 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    145
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
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)@comp28.ch.
                 Created on  5/28/12 at 12:52: 3 by user: wales       

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

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 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>  435 Cartesian coordinates will be optimised for  145 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=    -385.6845692     RMS force=    0.8484448404E-06
 OPTIM> Final energy  =    -385.3214596     RMS force=    0.7933364689E-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=     28617.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.59     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0790 Dev= 3.02% S= 35.79 time= 3.92
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  29.26
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     57235.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.59     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0241 Dev= 5.13% S= 39.89 time= 24.37
 Following    2 images are candidates for TS:   12   16  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         74
 Converged to TS (number of iterations):         69
 DNEB run yielded 2 true transition state(s) time=  16.52

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1121 steps. Energy=    -384.3610688       time=       4.00
 Minus side of path:                     966 steps. Energy=    -385.0762114       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3610688 0.94493         -383.4161356  1.6601         -385.0762114  28.423  26.737   4.410  32.883
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     992 steps. Energy=    -384.3610688       time=       3.75
 Minus side of path:                    1112 steps. Energy=    -385.3214596       time=       3.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.3610688  2.5820         -381.7790861  3.5424         -385.3214596  29.633  13.222   4.106  35.318
        Known (#3)                                              Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     63.580    
 decide> The unconnected minima in the chain and their distances are:
     4        3.99     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1913 Dev= 0.71% S= 4.33 time= 0.19
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   6.87

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1024 steps. Energy=    -385.0762114       time=       3.49
 Minus side of path:                     906 steps. Energy=    -383.4990014       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0762114  1.5976         -383.4785811 0.20420E-01     -383.4990014  23.869  23.490   4.533  31.985
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     127.16    
 decide> The unconnected minima in the chain and their distances are:
     4        3.99     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 4_F using 9 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 315 RMS= 0.0266 Dev= 2.08% S= 5.11 time= 3.71
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   7.94
 isnewts> transition state is the same as number        3 energy=     -383.4785810678
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1022 steps. Energy=    -385.0762114       time=       2.96
 Minus side of path:                     892 steps. Energy=    -383.4990014       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0762114  1.5976         -383.4785811 0.20420E-01     -383.4990014  23.869  23.491   4.522  32.062
        Known (#4)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     190.74    
 decide> The unconnected minima in the chain and their distances are:
     4        3.99     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 4_F using 17 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.9705470377E-01
 Double-ended search iterations= 595 RMS= 0.0152 Dev= 3.81% S= 5.89 time= 13.39
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.48

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     922 steps. Energy=    -385.6845692       time=       2.17
 Minus side of path:                     954 steps. Energy=    -385.0762114       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.6845692  5.6845         -380.0001187  5.0761         -385.0762114   4.490   3.992  28.714   5.050
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -385.6845692  5.6845        -380.0001187  5.0761        -385.0762114   4.490   3.992  28.714   5.050
   1     -385.0762114  1.6601        -383.4161356 0.94493        -384.3610688  28.423  26.737   4.410  32.883
   2     -384.3610688  2.5820        -381.7790861  3.5424        -385.3214596  29.633  13.222   4.106  35.318

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               138.64
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             51907 time=          65.47 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       587 time=           2.93 %=  2.1
