
 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 10:39:48
  [-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=    -534.1997122     RMS force=    0.8640551824E-06
 OPTIM> Final energy  =    -531.5047794     RMS force=    0.9923316532E-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=     16683.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.55     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.1375 Dev= 2.89% S= 31.00 time= 3.47
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   6.85

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     720 steps. Energy=    -531.9013419       time=       1.84
 Minus side of path:                     941 steps. Energy=    -530.2881462       time=       2.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9013419  3.4095         -528.4918082  1.7963         -530.2881462  28.028  22.189   2.204  48.554
        *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      2 steps with      2 missing connections, weight=     7798.8    
 decide> The unconnected minima in the chain and their distances are:
     2       16.22     3     3       15.23     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 8.3240 Dev= 0.51% S= 18.15 time= 1.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   6.92
 isnewts> transition state is the same as number        1 energy=     -528.4918081891
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     920 steps. Energy=    -530.2881462       time=       2.49
 Minus side of path:                     710 steps. Energy=    -531.9013419       time=       1.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.2881462  1.7963         -528.4918082  3.4095         -531.9013419  28.033  22.200   2.191  48.843
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.2653 Dev= 0.70% S= 16.84 time= 1.14
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.37

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     606 steps. Energy=    -534.1997122       time=       1.49
 Minus side of path:                     618 steps. Energy=    -533.2726971       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122  2.7271         -531.4726287  1.8001         -533.2726971  11.226   9.992  12.156   8.802
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     9049.5    
 decide> The unconnected minima in the chain and their distances are:
     2       19.57     4     3       11.58     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2193 Dev= 0.20% S= 20.89 time= 1.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=   9.94

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     663 steps. Energy=    -531.6968194       time=       1.67
 Minus side of path:                     677 steps. Energy=    -531.9282653       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.6968194 0.44502         -531.2518018 0.67646         -531.9282653  18.139  15.838   6.510  16.436
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.1359 Dev= 1.05% S= 12.87 time= 0.63
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        110
 DNEB run yielded 1 true transition state(s) time=  10.94

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     591 steps. Energy=    -534.5519477       time=       1.45
 Minus side of path:                     586 steps. Energy=    -535.1937886       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5519477 0.31802         -534.2339230 0.95987         -535.1937886   8.326   8.171   4.063  26.333
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     7921.5    
 decide> The unconnected minima in the chain and their distances are:
     2        4.08     6     6       16.81     3     3       11.58     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2106 Dev= 0.07% S= 4.17 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.42

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     582 steps. Energy=    -531.5047794       time=       1.42
 Minus side of path:                     648 steps. Energy=    -531.6968194       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.5047794 0.74169E-01     -531.4306099 0.26621         -531.6968194   4.519   4.078   8.787  12.177
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_U and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1908 Dev= 0.30% S= 19.07 time= 1.83
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  22.90

 tryconnect> 805-iteration DNEB run for minima 3_U and 5_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 805 RMS= 0.1750 Dev= 27.23% S= 21.13 time= 37.39
 Following    2 images are candidates for TS:    1   14  
 Converged to TS (number of iterations):         20
 Converged to TS (number of iterations):         29
 DNEB run yielded 2 true transition state(s) time=   6.71

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     605 steps. Energy=    -531.9013419       time=       1.48
 Minus side of path:                     681 steps. Energy=    -534.6241129       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9013419 0.25033E-01     -531.8763090  2.7478         -534.6241129   6.764   6.023   9.836  10.878
        Known (#3)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     606 steps. Energy=    -533.2726971       time=       1.49
 Minus side of path:                     598 steps. Energy=    -535.2494145       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2726971 0.34928         -532.9234135  2.3260         -535.2494145   6.242   4.747  14.420   7.420
        Known (#5)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     6780.8    
 decide> The unconnected minima in the chain and their distances are:
     2       17.60    10     3       10.99    11 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 10_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2302 Dev= 0.78% S= 19.89 time= 1.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  11.45

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     629 steps. Energy=    -530.6506651       time=       1.57
 Minus side of path:                     647 steps. Energy=    -531.3049587       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.6506651 0.14941         -530.5012543 0.80370         -531.3049587   6.848   5.770  29.510   3.626
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 11_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5291 Dev= 1.40% S= 12.57 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   7.46
 isnewts> transition state is the same as number        7 energy=     -531.8763089572
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     664 steps. Energy=    -534.6241129       time=       1.67
 Minus side of path:                     605 steps. Energy=    -531.9013419       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129  2.7478         -531.8763090 0.25033E-01     -531.9013419   6.764   6.024   9.825  10.890
        Known (#10)                                             Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     7509.9    
 decide> The unconnected minima in the chain and their distances are:
     6       18.27    10    10       11.21    11 
 

 tryconnect> 175-iteration DNEB run for minima 6_F and 10_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1799 Dev= 0.84% S= 20.51 time= 1.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   8.50

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     762 steps. Energy=    -531.9282653       time=       2.01
 Minus side of path:                     738 steps. Energy=    -530.2881462       time=       1.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9282653  2.1306         -529.7976543 0.49049         -530.2881462  29.251  26.497   5.195  20.598
        Known (#7)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 10_F and 11_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3996 Dev= 1.18% S= 12.57 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     646 steps. Energy=    -534.6241129       time=       1.68
 Minus side of path:                     615 steps. Energy=    -535.2494145       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129 0.74011         -533.8840039  1.3654         -535.2494145  14.145  11.232   9.054  11.819
        Known (#10)                                             Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -534.1997122  2.7271        -531.4726287  1.8001        -533.2726971  11.226   9.992  12.156   8.802
   8     -533.2726971 0.34928        -532.9234135  2.3260        -535.2494145   6.242   4.747  14.420   7.420
  12     -535.2494145  1.3654        -533.8840039 0.74011        -534.6241129  14.145  11.232   9.054  11.819
   7     -534.6241129  2.7478        -531.8763090 0.25033E-01    -531.9013419   6.764   6.023   9.836  10.878
   1     -531.9013419  3.4095        -528.4918082  1.7963        -530.2881462  28.028  22.189   2.204  48.554
  11     -530.2881462 0.49049        -529.7976543  2.1306        -531.9282653  29.251  26.497   5.195  20.598
   4     -531.9282653 0.67646        -531.2518018 0.44502        -531.6968194  18.139  15.838   6.510  16.436
   6     -531.6968194 0.26621        -531.4306099 0.74169E-01    -531.5047794   4.519   4.078   8.787  12.177

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

 Elapsed time=                               198.94
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             52429 time=         104.80 %= 52.7
 OPTIM> # of energy+gradient+Hessian calls=      1028 time=          56.38 %= 28.3
