
 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)@comp34.ch.
                 Created on  5/28/12 at 12:56: 1 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


 natintsetup, NATOMS          145
 cartres           12
 KeyInt>> Using natural internal coordinates. # of coords =        429
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         50      4500
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -384.8119039     RMS force=    0.9802004810E-06
 OPTIM> Final energy  =    -384.6621550     RMS force=    0.9449818968E-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=     43434.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.15     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1043 Dev= 2.16% S= 39.35 time= 4.91
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   7.85

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1014 steps. Energy=    -385.9653714       time=       4.02
 Minus side of path:                     965 steps. Energy=    -385.6241796       time=       3.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.9653714  1.8534         -384.1119856  1.5122         -385.6241796  19.937  18.434   2.734  53.027
        *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=     13036.    
 decide> The unconnected minima in the chain and their distances are:
     2       20.66     4     3       16.16     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0274 Dev= 0.14% S= 20.96 time= 1.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   6.45

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     939 steps. Energy=    -384.6621550       time=       4.01
 Minus side of path:                    1138 steps. Energy=    -385.6241796       time=       3.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.6621550 0.81941E-01     -384.5802145  1.0440         -385.6241796  22.641  20.669   3.018  48.038
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1297 Dev= 0.13% S= 16.61 time= 0.81
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   5.58

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     983 steps. Energy=    -386.5940331       time=       4.35
 Minus side of path:                     960 steps. Energy=    -385.3728640       time=       4.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5940331  3.0824         -383.5116760  1.8612         -385.3728640  17.106  10.925   5.337  27.169
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1301.5    
 decide> The unconnected minima in the chain and their distances are:
     3        6.08     5     6       10.25     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0410 Dev= 0.07% S= 6.09 time= 0.26
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     981 steps. Energy=    -386.5940331       time=       2.43
 Minus side of path:                     874 steps. Energy=    -385.9653714       time=       2.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.5940331 0.64899         -385.9450425 0.20329E-01     -385.9653714   6.186   6.085   2.369  61.220
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0418 Dev= 0.01% S= 10.27 time= 0.48
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   4.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     964 steps. Energy=    -384.8119039       time=       2.79
 Minus side of path:                     940 steps. Energy=    -385.3728640       time=       3.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -384.8119039 0.59681E-01     -384.7522224 0.62064         -385.3728640  10.505  10.248   2.216  65.435
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -384.8119039 0.59681E-01    -384.7522224 0.62064        -385.3728640  10.505  10.248   2.216  65.435
   3     -385.3728640  1.8612        -383.5116760  3.0824        -386.5940331  17.106  10.925   5.337  27.169
   4     -386.5940331 0.64899        -385.9450425 0.20329E-01    -385.9653714   6.186   6.085   2.369  61.220
   1     -385.9653714  1.8534        -384.1119856  1.5122        -385.6241796  19.937  18.434   2.734  53.027
   2     -385.6241796  1.0440        -384.5802145 0.81941E-01    -384.6621550  22.641  20.669   3.018  48.038

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

 Elapsed time=                                69.95
 OPTIM> # of energy calls=                         50 time=           0.07 %=  0.1
 OPTIM> # of energy+gradient calls=             20571 time=          27.36 %= 39.1
 OPTIM> # of energy+gradient+Hessian calls=       181 time=           0.87 %=  1.2
