
 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 12:01:05
  [-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=    -534.4494624     RMS force=    0.8973323401E-06
 OPTIM> Final energy  =    -535.2737449     RMS force=    0.8489164583E-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=     6763.7    
 decide> The unconnected minima in the chain and their distances are:
     2       18.91     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2453 Dev= 1.59% S= 24.71 time= 1.79
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.63

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     852 steps. Energy=    -535.8806147       time=       2.23
 Minus side of path:                     637 steps. Energy=    -531.8981753       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.8806147  4.2853         -531.5953513 0.30282         -531.8981753  25.111  19.252   6.810  15.712
        *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=     12242.    
 decide> The unconnected minima in the chain and their distances are:
     2       14.70     4     4       20.85     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1769 Dev= 0.27% S= 16.49 time= 1.16
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.99
 isnewts> transition state is the same as number        1 energy=     -531.5953513277
 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:                     654 steps. Energy=    -531.8981753       time=       1.63
 Minus side of path:                     825 steps. Energy=    -535.8806147       time=       2.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8981753 0.30282         -531.5953513  4.2853         -535.8806147  25.108  19.245   6.963  15.368
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2807 Dev= 0.62% S= 22.63 time= 2.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        158
 DNEB run yielded 1 true transition state(s) time=  16.27

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     639 steps. Energy=    -530.9988259       time=       1.65
 Minus side of path:                     831 steps. Energy=    -535.6419524       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.9988259 0.69160         -530.3072281  5.3347         -535.6419524  36.875  35.075   1.710  62.557
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     6326.0    
 decide> The unconnected minima in the chain and their distances are:
     2       10.80     6     6       17.17     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 3.9857 Dev= 0.77% S= 15.47 time= 0.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     608 steps. Energy=    -535.9353165       time=       1.52
 Minus side of path:                     589 steps. Energy=    -535.6419524       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.9353165 0.39877         -535.5365475 0.10540         -535.6419524   6.413   6.050   5.398  19.821
        *NEW* (Placed in 7)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2013 Dev= 0.22% S= 18.69 time= 1.79
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.55

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     631 steps. Energy=    -534.0047049       time=       1.61
 Minus side of path:                     675 steps. Energy=    -536.0457540       time=       1.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.0047049  1.2930         -532.7117092  3.3340         -536.0457540  19.402  17.905   3.994  26.793
        *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=     2328.5    
 decide> The unconnected minima in the chain and their distances are:
     2       11.52     7     7        8.91     9     8        4.52     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4890 Dev= 0.29% S= 16.06 time= 0.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.46
 isnewts> transition state is the same as number        4 energy=     -535.5365474647
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     588 steps. Energy=    -535.9353165       time=       1.46
 Minus side of path:                     582 steps. Energy=    -535.6419524       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.9353165 0.39877         -535.5365475 0.10540         -535.6419524   6.413   6.050   5.396  19.828
        Known (#7)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 9_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1804 Dev= 0.05% S= 8.98 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.68

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     600 steps. Energy=    -536.0457540       time=       1.47
 Minus side of path:                     638 steps. Energy=    -535.9353165       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0457540 0.62404         -535.4217169 0.51360         -535.9353165   9.640   8.914   4.332  24.701
        Known (#9)                                              Known (#7)
 Connection established between members of the U 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      6.139132535    
 Double-ended search iterations= 70 RMS= 0.4160 Dev= 0.87% S= 5.06 time= 0.30
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  26.46
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2704.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.80     6     8        4.52     1 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_U using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2118582465    
 Double-ended search iterations= 805 RMS= 0.0469 Dev= 3.63% S= 23.77 time= 37.20
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.43

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     618 steps. Energy=    -533.9384253       time=       1.51
 Minus side of path:                     643 steps. Energy=    -535.6419524       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9384253  3.0801         -530.8583316  4.7836         -535.6419524  18.302  13.756  10.034  10.664
        *NEW* (Placed in 10)                                    Known (#6)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 8_U using 10 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 350 RMS= 0.0363 Dev= 1.84% S= 6.17 time= 7.08
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.53

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     603 steps. Energy=    -534.4494624       time=       1.53
 Minus side of path:                     636 steps. Energy=    -534.0047049       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4494624  8.5368         -525.9126389  8.0921         -534.0047049   4.949   4.524  23.796   4.497
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     443.38    
 decide> The unconnected minima in the chain and their distances are:
     2        7.63    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1531 Dev= 0.19% S= 7.66 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.62

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     587 steps. Energy=    -533.9384253       time=       1.44
 Minus side of path:                     608 steps. Energy=    -535.2992868       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9384253 0.57092E-01     -533.8813331  1.4180         -535.2992868   7.308   7.199   4.794  22.319
        Known (#10)                                             *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1.2070    
 decide> The unconnected minima in the chain and their distances are:
     2        1.06    11 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0454 Dev= 0.04% S= 1.06 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):          8
 DNEB run yielded 1 true transition state(s) time=   1.83

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     531 steps. Energy=    -535.2992868       time=       1.28
 Minus side of path:                     536 steps. Energy=    -535.2737449       time=       1.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2992868 0.26810E-01     -535.2724771 0.12678E-02     -535.2737449   1.069   1.065   6.901  15.505
        Known (#11)                                             Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -534.4494624  8.5368        -525.9126389  8.0921        -534.0047049   4.949   4.524  23.796   4.497
   5     -534.0047049  1.2930        -532.7117092  3.3340        -536.0457540  19.402  17.905   3.994  26.793
   7     -536.0457540 0.62404        -535.4217169 0.51360        -535.9353165   9.640   8.914   4.332  24.701
   4     -535.9353165 0.39877        -535.5365475 0.10540        -535.6419524   6.413   6.050   5.398  19.821
   8     -535.6419524  4.7836        -530.8583316  3.0801        -533.9384253  18.302  13.756  10.034  10.664
  10     -533.9384253 0.57092E-01    -533.8813331  1.4180        -535.2992868   7.308   7.199   4.794  22.319
  11     -535.2992868 0.26810E-01    -535.2724771 0.12678E-02    -535.2737449   1.069   1.065   6.901  15.505

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

 Elapsed time=                               180.59
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             50959 time=         101.26 %= 56.1
 OPTIM> # of energy+gradient+Hessian calls=       823 time=          44.58 %= 24.7
