
 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 10:03:13
  [-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=    -531.5439001     RMS force=    0.9999284530E-06
 OPTIM> Final energy  =    -533.0600040     RMS force=    0.8536854265E-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=     16247.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.33     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.3047 Dev= 0.41% S= 34.72 time= 3.54
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         84
 DNEB run yielded 1 true transition state(s) time=   8.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     781 steps. Energy=    -531.9909715       time=       2.05
 Minus side of path:                     756 steps. Energy=    -531.7485650       time=       1.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9909715  1.6441         -530.3469125  1.4017         -531.7485650  16.519  13.352   2.456  43.558
        *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=     13097.    
 decide> The unconnected minima in the chain and their distances are:
     2       20.07     3     4       17.12     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 3_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2579 Dev= 1.27% S= 27.83 time= 2.64
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        219
 DNEB run yielded 1 true transition state(s) time=  25.26

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     598 steps. Energy=    -535.6032949       time=       1.47
 Minus side of path:                     591 steps. Energy=    -535.6083367       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.6032949 0.27149E-02     -535.6005800 0.77567E-02     -535.6083367   2.133   2.095  33.149   3.228
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2685 Dev= 0.20% S= 18.08 time= 1.86
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   9.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     841 steps. Energy=    -531.7485650       time=       2.22
 Minus side of path:                     620 steps. Energy=    -531.3267406       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7485650  1.1816         -530.5669371 0.75980         -531.3267406   9.939   8.999  17.302   6.184
        Known (#4)                                              *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      3 steps with      2 missing connections, weight=     16066.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.01     4     7       13.06     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2155 Dev= 0.74% S= 32.50 time= 3.52
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        150
 DNEB run yielded 1 true transition state(s) time=  14.78

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     648 steps. Energy=    -530.7319678       time=       1.66
 Minus side of path:                     789 steps. Energy=    -532.0056158       time=       2.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7319678 0.68097E-02     -530.7251581  1.2805         -532.0056158  15.034  14.397   2.553  41.910
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2527 Dev= 0.02% S= 13.26 time= 0.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.49

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     641 steps. Energy=    -531.3267406       time=       1.59
 Minus side of path:                     668 steps. Energy=    -531.5439001       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.3267406 0.93794         -530.3888037  1.1551         -531.5439001  15.193  13.072   2.594  41.255
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     9024.0    
 decide> The unconnected minima in the chain and their distances are:
     2       20.74     9     9        4.67     3 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 9_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 3.8242 Dev= 1.33% S= 28.31 time= 2.62
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  27.27

 tryconnect> 70-iteration DNEB run for minima 3_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6644 Dev= 0.34% S= 5.32 time= 0.41
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     599 steps. Energy=    -532.0056158       time=       1.52
 Minus side of path:                     668 steps. Energy=    -531.9909715       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.0056158 0.65769E-01     -531.9398469 0.51125E-01     -531.9909715   5.309   4.678  30.748   3.480
        Known (#9)                                              Known (#3)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     8964.8    
 decide> The unconnected minima in the chain and their distances are:
     2       20.77     8 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 8_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.5594 Dev= 1.36% S= 28.36 time= 2.57
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=  11.67

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     636 steps. Energy=    -535.4617574       time=       1.56
 Minus side of path:                     685 steps. Energy=    -535.5195931       time=       1.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4617574  5.2903         -530.1714942  5.3481         -535.5195931  20.762  10.469  14.966   7.150
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     4562.7    
 decide> The unconnected minima in the chain and their distances are:
     2       13.51    10    11       12.80     9 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 10_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0909 Dev= 0.08% S= 13.76 time= 1.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.56

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     695 steps. Energy=    -535.4617574       time=       1.77
 Minus side of path:                     631 steps. Energy=    -533.0600040       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4617574  2.5859         -532.8758539 0.18415         -533.0600040  13.845  13.516   3.405  31.426
        Known (#10)                                             Known (#2)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 9_S and 11_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2313 Dev= 0.18% S= 13.11 time= 0.74
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     632 steps. Energy=    -532.0056158       time=       1.56
 Minus side of path:                     614 steps. Energy=    -535.3020583       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.0056158 0.16765         -531.8379686  3.4641         -535.3020583   6.411   5.973   3.892  27.495
        Known (#9)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     2529.5    
 decide> The unconnected minima in the chain and their distances are:
    11       13.63     3 
 

 tryconnect> 140-iteration DNEB run for minima 3_S and 11_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2376 Dev= 0.22% S= 14.30 time= 1.23
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     610 steps. Energy=    -531.9909715       time=       1.51
 Minus side of path:                     604 steps. Energy=    -535.2770355       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9909715 0.17883         -531.8121439  3.4649         -535.2770355   6.415   5.957   3.934  27.197
        Known (#3)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     2781.5    
 decide> The unconnected minima in the chain and their distances are:
    11       14.06    12 
 

 tryconnect> 140-iteration DNEB run for minima 11_F and 12_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0675 Dev= 0.05% S= 14.31 time= 1.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.02

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     637 steps. Energy=    -535.5195931       time=       1.57
 Minus side of path:                     618 steps. Energy=    -535.3020583       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5195931 0.96002         -534.5595769 0.74248         -535.3020583  14.647  14.071   2.193  48.798
        Known (#11)                                             Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -531.5439001  1.1551        -530.3888037 0.93794        -531.3267406  15.193  13.072   2.594  41.255
   3     -531.3267406 0.75980        -530.5669371  1.1816        -531.7485650   9.939   8.999  17.302   6.184
   1     -531.7485650  1.4017        -530.3469125  1.6441        -531.9909715  16.519  13.352   2.456  43.558
   6     -531.9909715 0.51125E-01    -531.9398469 0.65769E-01    -532.0056158   5.309   4.678  30.748   3.480
   9     -532.0056158 0.16765        -531.8379686  3.4641        -535.3020583   6.411   5.973   3.892  27.495
  11     -535.3020583 0.74248        -534.5595769 0.96002        -535.5195931  14.647  14.071   2.193  48.798
   7     -535.5195931  5.3481        -530.1714942  5.2903        -535.4617574  20.762  10.469  14.966   7.150
   8     -535.4617574  2.5859        -532.8758539 0.18415        -533.0600040  13.845  13.516   3.405  31.426

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

 Elapsed time=                               178.90
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             37054 time=          74.40 %= 41.6
 OPTIM> # of energy+gradient+Hessian calls=      1100 time=          59.53 %= 33.3
