
 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 09:57:19
  [-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=    -535.4681083     RMS force=    0.9839018966E-06
 OPTIM> Final energy  =    -532.6546391     RMS force=    0.9672851490E-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=     2463.3    
 decide> The unconnected minima in the chain and their distances are:
     2       13.51     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.9000 Dev= 1.03% S= 19.38 time= 1.24
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=   9.36

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     755 steps. Energy=    -535.6613286       time=       1.93
 Minus side of path:                     605 steps. Energy=    -533.0196123       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.6613286  2.7703         -532.8910526 0.12856         -533.0196123   9.442   8.437   7.651  13.984
        *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=     2166.8    
 decide> The unconnected minima in the chain and their distances are:
     2       12.46     4     3        6.15     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4398 Dev= 0.77% S= 17.54 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.72

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     647 steps. Energy=    -533.0196123       time=       1.61
 Minus side of path:                     588 steps. Energy=    -532.7831742       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0196123 0.37746         -532.6421568 0.14102         -532.7831742   7.130   6.672   7.123  15.021
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2863 Dev= 0.17% S= 6.69 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.55

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     603 steps. Energy=    -535.3330929       time=       1.49
 Minus side of path:                     621 steps. Energy=    -535.4953243       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3330929 0.13328E-01     -535.3197644 0.17556         -535.4953243   5.253   4.796  14.236   7.516
        *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      6 steps with      3 missing connections, weight=     1133.8    
 decide> The unconnected minima in the chain and their distances are:
     2       10.34     5     3        2.94     7     6        1.37     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5678 Dev= 0.67% S= 15.94 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   9.32

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     609 steps. Energy=    -532.8527831       time=       1.52
 Minus side of path:                     521 steps. Energy=    -531.3059162       time=       1.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.8527831  1.5724         -531.2803834 0.25533E-01     -531.3059162   7.612   7.409   2.281  46.914
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.8735 Dev= 2.99% S= 3.47 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.59

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     570 steps. Energy=    -535.5295415       time=       1.39
 Minus side of path:                     580 steps. Energy=    -535.4953243       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5295415 0.61590         -534.9136368 0.58169         -535.4953243   8.418   8.315   7.179  14.905
        *NEW* (Placed in 10)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5101 Dev= 0.06% S= 1.38 time= 0.35
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.38
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1955.2    
 decide> The unconnected minima in the chain and their distances are:
     2       12.49     7     6        1.37     1 
 

 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= 0.5493 Dev= 0.70% S= 17.73 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   6.12

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     700 steps. Energy=    -535.4681083       time=       1.77
 Minus side of path:                     595 steps. Energy=    -532.8463297       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4681083  2.7245         -532.7435834 0.10275         -532.8463297   7.804   6.479   8.056  13.282
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_U using 3 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0386 Dev= 0.06% S= 1.38 time= 0.71
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.05
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1796.2    
 decide> The unconnected minima in the chain and their distances are:
     2       12.16    11 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 11_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5597 Dev= 0.79% S= 17.53 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.14

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     574 steps. Energy=    -532.6546391       time=       1.40
 Minus side of path:                     680 steps. Energy=    -532.8463297       time=       1.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6546391 0.18361         -532.4710308 0.37530         -532.8463297   7.583   7.045   6.594  16.227
        *NEW* (Placed in 12)                                    Known (#11)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     974.34    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91    12 
 

 checkpair> Energies of the minima in the pair     2   12 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.0457 Dev= 0.94% S= 15.50 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   4.96

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     689 steps. Energy=    -532.7831742       time=       1.73
 Minus side of path:                     658 steps. Energy=    -532.6546391       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7831742  5.9058         -526.8773602  5.7773         -532.6546391  22.518  10.551  13.339   8.022
        *NEW* (Placed in 13)                                    Known (#12)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 13 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     32.469    
 decide> The unconnected minima in the chain and their distances are:
     2        3.19    13 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 13_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.4157 Dev= 1.86% S= 3.80 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.75

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     609 steps. Energy=    -532.8527831       time=       1.54
 Minus side of path:                     628 steps. Energy=    -532.7831742       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.8527831 0.38325         -532.4695359 0.31364         -532.7831742   9.911   8.756   5.346  20.016
        *NEW* (Placed in 14)                                    Known (#13)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     64.939    
 decide> The unconnected minima in the chain and their distances are:
     2        3.19    13 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 13_S using 7 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.0815 Dev= 1.64% S= 4.64 time= 3.58
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):          8
 DNEB run yielded 1 true transition state(s) time=   1.95

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     632 steps. Energy=    -532.6546391       time=       1.56
 Minus side of path:                     577 steps. Energy=    -532.7831742       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6546391  8.3744         -524.2802540  8.5029         -532.7831742   3.596   3.191  41.304   2.591
        Known (#2)                                              Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -535.4681083  2.7245        -532.7435834 0.10275        -532.8463297   7.804   6.479   8.056  13.282
   7     -532.8463297 0.37530        -532.4710308 0.18361        -532.6546391   7.583   7.045   6.594  16.227
   8     -532.6546391  5.7773        -526.8773602  5.9058        -532.7831742  22.518  10.551  13.339   8.022
  10     -532.7831742  8.5029        -524.2802540  8.3744        -532.6546391   3.596   3.191  41.304   2.591

 Number of TS in the path       =      4
 Number of cycles               =      8

 Elapsed time=                               149.48
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             27135 time=          54.75 %= 36.6
 OPTIM> # of energy+gradient+Hessian calls=      1077 time=          58.19 %= 38.9
