
 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)@comp27.ch.
                 Created on  5/28/12 at 12:59:14 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=    -386.6466841     RMS force=    0.9886400717E-06
 OPTIM> Final energy  =    -391.7815997     RMS force=    0.9914255053E-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=     36837.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.27     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= 0.2381 Dev= 0.60% S= 35.72 time= 3.69
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.48

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1102 steps. Energy=    -386.6466841       time=       3.07
 Minus side of path:                    1349 steps. Energy=    -390.6161509       time=       6.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.6466841  2.2419         -384.4047873  6.2114         -390.6161509  39.585  36.097   2.380  60.919
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     580.34    
 decide> The unconnected minima in the chain and their distances are:
     2        8.34     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.3823 Dev= 0.28% S= 8.62 time= 0.19
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  20.65
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1160.7    
 decide> The unconnected minima in the chain and their distances are:
     2        8.34     3 
 

 tryconnect> 665-iteration DNEB run for minima 2_F and 3_S using 19 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      73.91988148    
 Double-ended search iterations= 665 RMS= 0.3799 Dev= 1.72% S= 8.91 time= 17.25
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     937 steps. Energy=    -391.5417108       time=       2.71
 Minus side of path:                     923 steps. Energy=    -390.6161509       time=       2.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.5417108  3.2526         -388.2890624  2.3271         -390.6161509   6.098   5.326  33.813   4.288
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1636.5    
 decide> The unconnected minima in the chain and their distances are:
     2       11.78     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.1513 Dev= 0.46% S= 12.13 time= 0.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     890 steps. Energy=    -391.5417108       time=       3.51
 Minus side of path:                     926 steps. Energy=    -391.9827399       time=       3.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.5417108  2.2095         -389.3322404  2.6505         -391.9827399  10.157   9.166  20.720   6.998
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     135.25    
 decide> The unconnected minima in the chain and their distances are:
     2        5.13     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0612 Dev= 0.44% S= 5.14 time= 0.20
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.38

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     937 steps. Energy=    -391.9409877       time=       2.17
 Minus side of path:                     919 steps. Energy=    -391.7815997       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9409877 0.18310         -391.7578901 0.23710E-01     -391.7815997   2.314   2.247  12.376  11.716
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     40.937    
 decide> The unconnected minima in the chain and their distances are:
     6        3.45     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0079 Dev= 0.13% S= 3.45 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     842 steps. Energy=    -391.9409877       time=       2.68
 Minus side of path:                     885 steps. Energy=    -391.9827399       time=       3.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -391.9409877 0.19023E-02     -391.9390854 0.43655E-01     -391.9827399   3.488   3.446   6.407  22.630
        Known (#6)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -386.6466841  2.2419        -384.4047873  6.2114        -390.6161509  39.585  36.097   2.380  60.919
   2     -390.6161509  2.3271        -388.2890624  3.2526        -391.5417108   6.098   5.326  33.813   4.288
   3     -391.5417108  2.2095        -389.3322404  2.6505        -391.9827399  10.157   9.166  20.720   6.998
   5     -391.9827399 0.43655E-01    -391.9390854 0.19023E-02    -391.9409877   3.488   3.446   6.407  22.630
   4     -391.9409877 0.18310        -391.7578901 0.23710E-01    -391.7815997   2.314   2.247  12.376  11.716

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                                95.50
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             32210 time=          42.32 %= 44.3
 OPTIM> # of energy+gradient+Hessian calls=       388 time=           1.94 %=  2.0
