
 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 10:39:08
  [-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=    -534.3727543     RMS force=    0.9207145421E-06
 OPTIM> Final energy  =    -538.1338451     RMS force=    0.9870879531E-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=     2487.4    
 decide> The unconnected minima in the chain and their distances are:
     2       13.55     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 4.8161 Dev= 0.76% S= 19.73 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  10.82

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     611 steps. Energy=    -538.8871812       time=       1.50
 Minus side of path:                     603 steps. Energy=    -536.2293838       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8871812  3.2307         -535.6565229 0.57286         -536.2293838   9.697   9.386   4.292  24.928
        *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=     4974.9    
 decide> The unconnected minima in the chain and their distances are:
     2       13.55     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 805 RMS= 0.2013 Dev= 3.71% S= 24.99 time= 36.71
 Following    2 images are candidates for TS:    4   15  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):        118
 DNEB run yielded 2 true transition state(s) time=  15.33

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     616 steps. Energy=    -536.0067185       time=       1.54
 Minus side of path:                     617 steps. Energy=    -534.3727543       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0067185  4.2354         -531.7713439  2.6014         -534.3727543  10.356   6.703  15.281   7.002
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     596 steps. Energy=    -536.7428797       time=       1.46
 Minus side of path:                     566 steps. Energy=    -539.1749963       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.7428797 0.56679         -536.1760910  2.9989         -539.1749963   9.954   9.034   4.313  24.807
        *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=     1680.1    
 decide> The unconnected minima in the chain and their distances are:
     2       11.89     5 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 1.8816 Dev= 0.15% S= 17.55 time= 0.55
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=   9.87

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     672 steps. Energy=    -538.1338451       time=       1.72
 Minus side of path:                     596 steps. Energy=    -536.0067185       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1338451  2.5505         -535.5833575 0.42336         -536.0067185   9.293   6.577  16.896   6.333
        *NEW* (Placed in 8)                                     Known (#5)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     974.49    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     8 
 

 checkpair> Energies of the minima in the pair     2    8 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.0878 Dev= 4.52% S= 14.24 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     624 steps. Energy=    -536.7428797       time=       1.56
 Minus side of path:                     791 steps. Energy=    -538.1338451       time=       2.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.7428797  8.5408         -528.2020891  9.9318         -538.1338451  18.311  16.758   2.095  51.074
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1949.0    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     8 
 

 checkpair> Energies of the minima in the pair     2    8 are the same - checking distance ...

 tryconnect> 770-iteration DNEB run for minima 2_F and 8_S using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 770 RMS= 0.1741 Dev= 5.89% S= 21.87 time= 32.23
 Following    2 images are candidates for TS:    9   12  
 Converged to TS (number of iterations):         98
 Converged to TS (number of iterations):        127
 DNEB run yielded 2 true transition state(s) time=  23.16

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     627 steps. Energy=    -536.7428797       time=       1.54
 Minus side of path:                     694 steps. Energy=    -539.1749963       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.7428797 0.94593         -535.7969545  3.3780         -539.1749963  14.216   9.047   4.287  24.960
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     797 steps. Energy=    -538.1338451       time=       2.06
 Minus side of path:                     716 steps. Energy=    -538.8871812       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1338451  2.4738         -535.6600031  3.2272         -538.8871812  25.066  23.745   2.273  47.084
        Known (#8)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     979.57    
 decide> The unconnected minima in the chain and their distances are:
     7        9.91    10    10        1.75    11 
 

 checkpair> Energies of the minima in the pair     7   10 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 7_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.9661 Dev= 2.03% S= 14.52 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.67

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     629 steps. Energy=    -538.8871812       time=       1.55
 Minus side of path:                     600 steps. Energy=    -539.1749963       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8871812  8.6484         -530.2387856  8.9362         -539.1749963   5.947   1.749  83.262   1.285
        Known (#11)                                             Known (#10)
 Unconnected minimum 10 found its way to S set.
 newconnect> skipping DIJKSTRA pair number        2 minima       11      10 distance is now      0.000000000    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     974.27    
 decide> The unconnected minima in the chain and their distances are:
     6        9.91     9 
 

 checkpair> Energies of the minima in the pair     6    9 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 5.3817 Dev= 6.63% S= 14.41 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        129
 DNEB run yielded 1 true transition state(s) time=  11.68

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     788 steps. Energy=    -538.1338451       time=       2.02
 Minus side of path:                     724 steps. Energy=    -538.8871812       time=       1.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1338451  2.4738         -535.6600031  3.2272         -538.8871812  25.067  23.746   2.271  47.110
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     974.23    
 decide> The unconnected minima in the chain and their distances are:
     3        9.91    11 
 

 checkpair> Energies of the minima in the pair     3   11 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 3_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.5293 Dev= 2.40% S= 14.26 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   4.97

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     679 steps. Energy=    -538.8871812       time=       1.69
 Minus side of path:                     607 steps. Energy=    -539.1749963       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8871812  3.1391         -535.7481124  3.4269         -539.1749963  15.327  10.211  15.198   7.040
        Known (#11)                                             Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -534.3727543  2.6014        -531.7713439  4.2354        -536.0067185  10.356   6.703  15.281   7.002
   4     -536.0067185 0.42336        -535.5833575  2.5505        -538.1338451   9.293   6.577  16.896   6.333
   7     -538.1338451  2.4738        -535.6600031  3.2272        -538.8871812  25.066  23.745   2.273  47.084
  10     -538.8871812  3.1391        -535.7481124  3.4269        -539.1749963  15.327  10.211  15.198   7.040
   3     -539.1749963  2.9989        -536.1760910 0.56679        -536.7428797   9.954   9.034   4.313  24.807
   5     -536.7428797  8.5408        -528.2020891  9.9318        -538.1338451  18.311  16.758   2.095  51.074

 Number of TS in the path       =      6
 Number of cycles               =      8

 Elapsed time=                               191.62
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             57878 time=         114.70 %= 59.9
 OPTIM> # of energy+gradient+Hessian calls=       828 time=          45.33 %= 23.7
