
 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> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/24/2012 at 10:40:25
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    107
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    17
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 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>  321 Cartesian coordinates will be optimised for  107 AMBER 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=    -534.4293199     RMS force=    0.8601682588E-06
 OPTIM> Final energy  =    -530.7220740     RMS force=    0.9704368219E-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=     10053.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.58     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 210 RMS= 0.5650 Dev= 2.48% S= 27.45 time= 2.55
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        207
 DNEB run yielded 1 true transition state(s) time=  21.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     587 steps. Energy=    -534.5511486       time=       1.50
 Minus side of path:                     600 steps. Energy=    -535.5398588       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5511486 0.54635         -534.0048023  1.5351         -535.5398588   9.932   8.902   6.038  17.722
        *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      1 steps with      1 missing connections, weight=     20106.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.58     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.2313 Dev= 3.91% S= 41.16 time= 37.09
 Following    3 images are candidates for TS:    5   11   17  
 Converged to TS (number of iterations):         35
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         93
 DNEB run yielded 2 true transition state(s) time=  35.72

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     612 steps. Energy=    -532.3536434       time=       1.51
 Minus side of path:                     616 steps. Energy=    -534.4293199       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3536434  2.2606         -530.0930264  4.3363         -534.4293199   8.032   7.139   8.860  12.077
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     589 steps. Energy=    -535.1372754       time=       1.46
 Minus side of path:                     608 steps. Energy=    -534.7010185       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1372754  1.3572         -533.7800992 0.92092         -534.7010185  14.360  11.760   8.118  13.180
        *NEW* (Placed in 6)                                     *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      2 steps with      1 missing connections, weight=     10040.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.57     5 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 5_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 210 RMS= 1.9774 Dev= 1.38% S= 26.61 time= 2.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   8.63

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     610 steps. Energy=    -531.4992169       time=       1.50
 Minus side of path:                     640 steps. Energy=    -534.7010185       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.4992169  1.5814         -529.9178460  4.7832         -534.7010185  12.992  11.222   1.919  55.748
        *NEW* (Placed in 8)                                     Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     10172.    
 decide> The unconnected minima in the chain and their distances are:
     2       14.37     8     8       19.31     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 8_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 1.3480 Dev= 1.98% S= 18.80 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        168
 DNEB run yielded 1 true transition state(s) time=  16.71

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     612 steps. Energy=    -526.8466805       time=       1.50
 Minus side of path:                     677 steps. Energy=    -530.7220740       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -526.8466805 0.20164         -526.6450414  4.0770         -530.7220740  25.752  24.587   5.571  19.207
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 8_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.8046 Dev= 0.48% S= 22.80 time= 1.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=   9.74

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     852 steps. Energy=    -535.5521057       time=       2.23
 Minus side of path:                     910 steps. Energy=    -533.7220148       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5521057  4.3593         -531.1928234  2.5292         -533.7220148  30.795  25.610   4.113  26.017
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     5230.4    
 decide> The unconnected minima in the chain and their distances are:
     2       15.18     7     7       11.62    10    11        5.46     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 140 RMS= 1.2335 Dev= 1.13% S= 19.85 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.49

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     703 steps. Energy=    -534.6561164       time=       1.77
 Minus side of path:                     704 steps. Energy=    -534.7010185       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  5.6660         -528.9901570  5.7109         -534.7010185  25.712  10.571  13.281   8.057
        *NEW* (Placed in 12)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 7_U and 10_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2159 Dev= 0.09% S= 12.41 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.88

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     583 steps. Energy=    -534.6561164       time=       1.42
 Minus side of path:                     709 steps. Energy=    -535.5521057       time=       1.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164 0.67347         -533.9826503  1.5695         -535.5521057  12.990  11.557   7.287  14.683
        *NEW* (Placed in 13)                                    Known (#10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7661 Dev= 0.31% S= 5.68 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.65

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     641 steps. Energy=    -533.7220148       time=       1.58
 Minus side of path:                     603 steps. Energy=    -532.3536434       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7220148  1.6699         -532.0521062 0.30154         -532.3536434   5.913   5.463  11.561   9.256
        Known (#11)                                             Known (#5)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1733.2    
 decide> The unconnected minima in the chain and their distances are:
     2       11.95    12     7        2.94    13 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 12_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.2223 Dev= 0.42% S= 13.13 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=   9.93

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     894 steps. Energy=    -534.6561164       time=       2.37
 Minus side of path:                     619 steps. Energy=    -528.9808555       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  5.8776         -528.7785078 0.20235         -528.9808555  21.318  19.994   2.373  45.098
        Known (#12)                                             *NEW* (Placed in 14)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 13_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6561 Dev= 0.12% S= 3.57 time= 0.29
 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=  23.74
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     2614.8    
 decide> The unconnected minima in the chain and their distances are:
     2       13.69    14     7        2.94    13 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 14_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4984 Dev= 0.85% S= 14.55 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   6.98

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     549 steps. Energy=    -530.7220740       time=       1.33
 Minus side of path:                     865 steps. Energy=    -534.6561164       time=       2.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7220740 0.17791         -530.5441606  4.1120         -534.6561164  13.680  12.015   3.052  35.056
        Known (#2)                                              Known (#12)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 7_F and 13_S using 6 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 210 RMS= 0.0785 Dev= 3.42% S= 4.15 time= 2.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.16

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     583 steps. Energy=    -534.7010185       time=       1.43
 Minus side of path:                     601 steps. Energy=    -534.6561164       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7010185  8.3569         -526.3441422  8.3120         -534.6561164   3.560   2.939  38.498   2.779
        Known (#7)                                              Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -534.4293199  4.3363        -530.0930264  2.2606        -532.3536434   8.032   7.139   8.860  12.077
   9     -532.3536434 0.30154        -532.0521062  1.6699        -533.7220148   5.913   5.463  11.561   9.256
   6     -533.7220148  2.5292        -531.1928234  4.3593        -535.5521057  30.795  25.610   4.113  26.017
   8     -535.5521057  1.5695        -533.9826503 0.67347        -534.6561164  12.990  11.557   7.287  14.683
  12     -534.6561164  8.3120        -526.3441422  8.3569        -534.7010185   3.560   2.939  38.498   2.779
   7     -534.7010185  5.7109        -528.9901570  5.6660        -534.6561164  25.712  10.571  13.281   8.057
  11     -534.6561164  4.1120        -530.5441606 0.17791        -530.7220740  13.680  12.015   3.052  35.056

 Number of TS in the path       =      7
 Number of cycles               =      7

 Elapsed time=                               242.03
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             54711 time=         109.09 %= 45.1
 OPTIM> # of energy+gradient+Hessian calls=      1511 time=          81.96 %= 33.9
