
 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 11:59:33
  [-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.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.6191208     RMS force=    0.9683795423E-06
 OPTIM> Final energy  =    -532.9906145     RMS force=    0.8336857817E-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=    0.10375E+06
 decide> The unconnected minima in the chain and their distances are:
     2       46.99     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0478 Dev= 1.98% S= 53.35 time= 13.84
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.74

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1321 steps. Energy=    -534.0552065       time=       4.53
 Minus side of path:                     793 steps. Energy=    -533.1231560       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.0552065  3.4444         -530.6108490  2.5123         -533.1231560  47.253  42.799   2.082  51.388
        *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=     44811.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.57     4     4       31.06     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0838 Dev= 0.06% S= 26.25 time= 3.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   9.22

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     675 steps. Energy=    -532.5549985       time=       1.68
 Minus side of path:                     725 steps. Energy=    -532.5704640       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5549985 0.68890         -531.8661017 0.70436         -532.5704640  24.109  21.531   2.939  36.405
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 4_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0368 Dev= 1.19% S= 33.26 time= 5.74
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   8.83

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     603 steps. Energy=    -533.5603891       time=       1.49
 Minus side of path:                     628 steps. Energy=    -533.8931573       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5603891 0.91382E-02     -533.5512509 0.34191         -533.8931573   7.285   7.176   2.965  36.087
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     29649.    
 decide> The unconnected minima in the chain and their distances are:
     2       20.22     6     5       27.61     7     8        6.99     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2652 Dev= 0.16% S= 21.58 time= 2.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.18

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     789 steps. Energy=    -532.9906145       time=       2.08
 Minus side of path:                     665 steps. Energy=    -532.5704640       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9906145 0.93996         -532.0506585 0.51981         -532.5704640  23.004  20.267   2.213  48.357
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 5_F and 7_U using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 280 RMS= 0.2122 Dev= 0.65% S= 28.64 time= 4.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        107
 DNEB run yielded 1 true transition state(s) time=  11.33

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     643 steps. Energy=    -532.3400490       time=       1.62
 Minus side of path:                     659 steps. Energy=    -532.5704640       time=       1.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3400490 0.11445         -532.2256025 0.34486         -532.5704640   6.880   6.651   6.101  17.537
        *NEW* (Placed in 9)                                     Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1431 Dev= 0.31% S= 7.23 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.45

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     642 steps. Energy=    -533.6191208       time=       1.64
 Minus side of path:                     652 steps. Energy=    -533.8931573       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.6191208 0.30699         -533.3121319 0.58103         -533.8931573   8.641   6.990  14.253   7.507
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     23751.    
 decide> The unconnected minima in the chain and their distances are:
     5       16.22     4     4       26.91     7 
 

 tryconnect> 140-iteration DNEB run for minima 4_U and 5_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0806 Dev= 0.10% S= 16.74 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.60

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     667 steps. Energy=    -533.1231560       time=       1.67
 Minus side of path:                     997 steps. Energy=    -532.5704640       time=       2.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1231560  1.4298         -531.6933308 0.87713         -532.5704640  24.355  21.116   2.056  52.035
        Known (#4)                                              Known (#6)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 4_F and 7_S using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1408 Dev= 0.28% S= 28.18 time= 4.55
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   7.87

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     675 steps. Energy=    -533.3408020       time=       1.71
 Minus side of path:                     662 steps. Energy=    -533.5603891       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3408020 0.77874         -532.5620652 0.99832         -533.5603891  15.158  13.614   3.151  33.952
        *NEW* (Placed in 10)                                    Known (#7)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5846.9    
 decide> The unconnected minima in the chain and their distances are:
     4       18.02    10 
 

 tryconnect> 175-iteration DNEB run for minima 4_F and 10_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0541 Dev= 0.25% S= 18.47 time= 1.81
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   6.63

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     639 steps. Energy=    -533.1231560       time=       1.58
 Minus side of path:                     723 steps. Energy=    -533.5077046       time=       1.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1231560 0.71686E-01     -533.0514702 0.45623         -533.5077046  12.026  11.516   1.603  66.768
        Known (#4)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1243.0    
 decide> The unconnected minima in the chain and their distances are:
    11       10.75    10 
 

 tryconnect> 105-iteration DNEB run for minima 10_S and 11_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0490 Dev= 0.15% S= 10.81 time= 0.65
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.08

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     724 steps. Energy=    -533.3408020       time=       1.85
 Minus side of path:                     634 steps. Energy=    -533.0309019       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3408020 0.52074         -532.8200583 0.21084         -533.0309019  19.749  18.202   2.630  40.688
        Known (#10)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     2486.0    
 decide> The unconnected minima in the chain and their distances are:
    11       10.75    10 
 

 tryconnect> 805-iteration DNEB run for minima 10_S and 11_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1433940004    
 Double-ended search iterations= 439 RMS= 0.0010 Dev= 2.18% S= 11.05 time= 20.43
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):          7
 DNEB run yielded 1 true transition state(s) time=   1.84

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     611 steps. Energy=    -533.3408020       time=       1.53
 Minus side of path:                     768 steps. Energy=    -533.5077046       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3408020 0.11685E-03     -533.3406852 0.16702         -533.5077046  10.801  10.753   2.717  39.375
        Known (#10)                                             Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -533.6191208 0.30699        -533.3121319 0.58103        -533.8931573   8.641   6.990  14.253   7.507
   3     -533.8931573 0.34191        -533.5512509 0.91382E-02    -533.5603891   7.285   7.176   2.965  36.087
   8     -533.5603891 0.99832        -532.5620652 0.77874        -533.3408020  15.158  13.614   3.151  33.952
  11     -533.3408020 0.11685E-03    -533.3406852 0.16702        -533.5077046  10.801  10.753   2.717  39.375
   9     -533.5077046 0.45623        -533.0514702 0.71686E-01    -533.1231560  12.026  11.516   1.603  66.768
   7     -533.1231560  1.4298        -531.6933308 0.87713        -532.5704640  24.355  21.116   2.056  52.035
   4     -532.5704640 0.51981        -532.0506585 0.93996        -532.9906145  23.004  20.267   2.213  48.357

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

 Elapsed time=                               174.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             53434 time=         106.10 %= 60.8
 OPTIM> # of energy+gradient+Hessian calls=       688 time=          37.50 %= 21.5
