
 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 09:58:08
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -535.5404266     RMS force=    0.8451572902E-06
 OPTIM> Final energy  =    -537.3080266     RMS force=    0.8805576997E-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=     4901.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.99     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 1.6898 Dev= 0.15% S= 23.39 time= 1.89
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.42

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     644 steps. Energy=    -538.1093457       time=       1.63
 Minus side of path:                     614 steps. Energy=    -535.6613286       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1093457  5.8296         -532.2797391  3.3816         -535.6613286   9.459   6.269  13.277   8.059
        *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=     5527.6    
 decide> The unconnected minima in the chain and their distances are:
     2       17.51     3     4        5.42     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.4470 Dev= 1.57% S= 23.11 time= 1.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.76

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     662 steps. Energy=    -536.1647370       time=       1.65
 Minus side of path:                     661 steps. Energy=    -536.1617649       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.1647370  2.7200         -533.4447292  2.7170         -536.1617649  16.347  10.160  15.460   6.921
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1643 Dev= 0.16% S= 5.61 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.95

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     561 steps. Energy=    -535.5404266       time=       1.40
 Minus side of path:                     662 steps. Energy=    -535.6613286       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5404266 0.11087         -535.4295578 0.23177         -535.6613286   6.046   5.422  13.377   7.999
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5390.5    
 decide> The unconnected minima in the chain and their distances are:
     2       17.53     4 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3483 Dev= 0.37% S= 23.60 time= 1.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        160
 DNEB run yielded 1 true transition state(s) time=  15.89

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     673 steps. Energy=    -537.8519727       time=       1.68
 Minus side of path:                     721 steps. Energy=    -538.0396260       time=       1.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.8519727  1.1471         -536.7049155  1.3347         -538.0396260  13.519  10.711   3.936  27.187
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     3409.3    
 decide> The unconnected minima in the chain and their distances are:
     2       13.14     7     7       10.44     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.9977 Dev= 0.25% S= 13.73 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   7.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     648 steps. Energy=    -536.7365192       time=       1.61
 Minus side of path:                     694 steps. Energy=    -538.1093457       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.7365192 0.54225         -536.1942695  1.9151         -538.1093457  15.175  14.159   3.525  30.354
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5166 Dev= 0.22% S= 16.10 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.59

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     671 steps. Energy=    -536.5449196       time=       1.69
 Minus side of path:                     649 steps. Energy=    -536.5420368       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.5449196  2.7116         -533.8333492  2.7087         -536.5420368  16.805  10.174  15.556   6.878
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1462.8    
 decide> The unconnected minima in the chain and their distances are:
     2        7.88     9    10        9.91     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.6926 Dev= 0.20% S= 8.20 time= 0.38
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.16

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     602 steps. Energy=    -537.3080266       time=       1.51
 Minus side of path:                     635 steps. Energy=    -536.7365192       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.3080266 0.90946         -536.3985692 0.33795         -536.7365192   8.607   7.881   9.999  10.701
        Known (#2)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 checkpair> Energies of the minima in the pair     3   10 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 3_S and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9453 Dev= 0.56% S= 15.41 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   7.76

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     629 steps. Energy=    -536.5420368       time=       1.78
 Minus side of path:                     622 steps. Energy=    -536.2990436       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.5420368 0.36259         -536.1794453 0.11960         -536.2990436  11.837  11.647   6.574  16.277
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1609.8    
 decide> The unconnected minima in the chain and their distances are:
    10       11.72     4 
 

 tryconnect> 105-iteration DNEB run for minima 4_S and 10_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 4.4481 Dev= 0.96% S= 17.85 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.35

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     612 steps. Energy=    -535.4953243       time=       1.55
 Minus side of path:                     667 steps. Energy=    -537.8519727       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4953243  3.4647         -532.0306162  5.8214         -537.8519727   9.535   6.277  13.409   7.980
        *NEW* (Placed in 15)                                    Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 15 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     1139.7    
 decide> The unconnected minima in the chain and their distances are:
    10        3.52     7    15       10.31     4 
 

 tryconnect> 70-iteration DNEB run for minima 7_U and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 70 RMS= 1.7442 Dev= 2.51% S= 3.97 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.24

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     610 steps. Energy=    -537.8519727       time=       1.51
 Minus side of path:                     580 steps. Energy=    -537.7282404       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.8519727 0.15663         -537.6953385 0.32902E-01     -537.7282404   3.910   3.732  30.836   3.470
        Known (#7)                                              *NEW* (Placed in 16)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 15_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.2371 Dev= 1.12% S= 16.40 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.23

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     701 steps. Energy=    -535.6613286       time=       1.78
 Minus side of path:                     703 steps. Energy=    -535.4953243       time=       1.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.6613286  5.4743         -530.1870663  5.3083         -535.4953243  25.416  10.544  13.427   7.969
        Known (#4)                                              Known (#15)
 Unconnected minimum 15 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 16 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     87.420    
 decide> The unconnected minima in the chain and their distances are:
    10        3.52     7 
 

 tryconnect> 280-iteration DNEB run for minima 7_S and 10_F using 8 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 280 RMS= 0.0218 Dev= 4.68% S= 5.01 time= 4.61
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.06

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     603 steps. Energy=    -538.1093457       time=       1.48
 Minus side of path:                     614 steps. Energy=    -537.8519727       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1093457  8.4746         -529.6347579  8.2172         -537.8519727   3.899   3.523  34.566   3.096
        Known (#10)                                             Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -535.5404266 0.11087        -535.4295578 0.23177        -535.6613286   6.046   5.422  13.377   7.999
  11     -535.6613286  5.4743        -530.1870663  5.3083        -535.4953243  25.416  10.544  13.427   7.969
   9     -535.4953243  3.4647        -532.0306162  5.8214        -537.8519727   9.535   6.277  13.409   7.980
  12     -537.8519727  8.2172        -529.6347579  8.4746        -538.1093457   3.899   3.523  34.566   3.096
   5     -538.1093457  1.9151        -536.1942695 0.54225        -536.7365192  15.175  14.159   3.525  30.354
   7     -536.7365192 0.33795        -536.3985692 0.90946        -537.3080266   8.607   7.881   9.999  10.701

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

 Elapsed time=                               131.64
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             31068 time=          62.67 %= 47.6
 OPTIM> # of energy+gradient+Hessian calls=       719 time=          38.97 %= 29.6
