
 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 05/23/2012 at 21:11:29
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
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>  654 Cartesian coordinates will be optimised for  218 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=    -450.9076912     RMS force=    0.9332228671E-06
 OPTIM> Final energy  =    -448.6758498     RMS force=    0.8538351849E-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=    0.74390E+06
 decide> The unconnected minima in the chain and their distances are:
     2       90.61     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 805 RMS= 0.0584 Dev= 2.50% S= 112.36 time= 139.80
 Following    2 images are candidates for TS:    9   13  
 Converged to TS (number of iterations):        164
 Converged to TS (number of iterations):        187
 DNEB run yielded 2 true transition state(s) time= 179.02

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1308 steps. Energy=    -449.3248742       time=      14.25
 Minus side of path:                    1219 steps. Energy=    -446.5515015       time=      13.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3248742  2.7997         -446.5251384 0.26363E-01     -446.5515015  23.353  20.837   3.341  65.258
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    2023 steps. Energy=    -448.8204776       time=      30.21
 Minus side of path:                    1702 steps. Energy=    -446.6375222       time=      25.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8204776  2.9031         -445.9174065 0.72012         -446.6375222  66.246  62.118   1.879 116.011
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     92765.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.18     6     5       38.31     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 6_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1316 Dev= 1.56% S= 35.99 time= 21.64
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=  59.13

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1307 steps. Energy=    -447.4585935       time=      15.08
 Minus side of path:                    1295 steps. Energy=    -446.6128535       time=      17.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4585935 0.90170         -446.5568900 0.55964E-01     -446.6128535  18.808  18.433   2.090 104.310
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 5_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0503 Dev= 2.30% S= 41.72 time= 32.24
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        148
 DNEB run yielded 1 true transition state(s) time=  81.68

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1348 steps. Energy=    -448.8204776       time=      17.35
 Minus side of path:                    1945 steps. Energy=    -454.2913664       time=      25.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8204776 0.61557         -448.2049057  6.0865         -454.2913664  41.657  32.216   1.714 127.163
        Known (#5)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     88004.    
 decide> The unconnected minima in the chain and their distances are:
     2        7.92     7     8       25.71     6     9       41.32     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.5507 Dev= 0.40% S= 8.83 time= 1.06
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=  23.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1302 steps. Energy=    -447.4585935       time=      14.26
 Minus side of path:                    1303 steps. Energy=    -448.3370061       time=      14.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4585935  3.0986         -444.3600247  3.9770         -448.3370061   8.867   7.678  29.018   7.512
        Known (#7)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 6_U and 8_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0264 Dev= 0.02% S= 25.86 time= 12.95
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  34.95

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1267 steps. Energy=    -446.6375222       time=      16.34
 Minus side of path:                    1287 steps. Energy=    -446.6128535       time=      16.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.6375222 0.20316         -446.4343597 0.17849         -446.6128535  26.493  25.719   1.823 119.565
        Known (#6)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 420-iteration DNEB run for minima 1_S and 9_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0483 Dev= 1.96% S= 47.24 time= 37.74
 Following    2 images are candidates for TS:    3    8  
 Converged to TS (number of iterations):        157
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time= 133.43

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1234 steps. Energy=    -452.8125449       time=      16.03
 Minus side of path:                    1301 steps. Energy=    -453.1982270       time=      16.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8125449 0.80814E-01     -452.7317307 0.46650         -453.1982270  16.146  15.160   2.254  96.721
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1236 steps. Energy=    -452.6298675       time=      13.96
 Minus side of path:                    1330 steps. Energy=    -452.7869308       time=      16.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.6298675  2.2424         -450.3874814  2.3994         -452.7869308  30.812  29.198   2.456  88.762
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 14 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      4 missing connections, weight=     21659.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.83    10     9       14.52    13    14        1.65    11    12       26.49     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1218 Dev= 0.22% S= 1.97 time= 1.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  24.57

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1294 steps. Energy=    -448.3370061       time=      17.82
 Minus side of path:                    1285 steps. Energy=    -448.6758498       time=      13.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3370061 0.54727         -447.7897362 0.88611         -448.6758498   1.996   1.828  98.935   2.203
        Known (#10)                                             Known (#2)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 9_F and 13_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1175 Dev= 0.15% S= 14.66 time= 4.21
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  24.89

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1304 steps. Energy=    -454.2913664       time=      14.31
 Minus side of path:                    1263 steps. Energy=    -452.6298675       time=      13.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2913664  1.7628         -452.5286058 0.10126         -452.6298675  15.578  14.524   3.327  65.520
        Known (#9)                                              Known (#13)
 Unconnected minimum 13 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 11_U and 14_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0752 Dev= 0.18% S= 1.79 time= 1.06
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=  18.63

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1234 steps. Energy=    -452.7869308       time=      13.88
 Minus side of path:                    1215 steps. Energy=    -452.8125449       time=      14.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.7869308 0.76255         -452.0243793 0.78817         -452.8125449   1.828   1.647 145.148   1.502
        Known (#14)                                             Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 12_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1139 Dev= 0.62% S= 27.80 time= 13.00
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=  35.07

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1449 steps. Energy=    -453.1855420       time=      19.35
 Minus side of path:                    1243 steps. Energy=    -450.9076912       time=      15.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1855420  2.2975         -450.8880556 0.19636E-01     -450.9076912  20.160  18.985   3.454  63.121
        *NEW* (Placed in 15)                                    Known (#1)
 Unconnected minimum 15 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 15 minima and 12 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      1 missing connections, weight=     2650.0    
 decide> The unconnected minima in the chain and their distances are:
    12       13.84    15 
 

 tryconnect> 140-iteration DNEB run for minima 12_F and 15_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0221 Dev= 0.02% S= 13.87 time= 4.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  29.84

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                    1278 steps. Energy=    -453.1855420       time=      15.21
 Minus side of path:                    1267 steps. Energy=    -453.1982270       time=      16.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1855420 0.27199         -452.9135526 0.28467         -453.1982270  14.384  13.839   2.349  92.815
        Known (#15)                                             Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  12     -450.9076912 0.19636E-01    -450.8880556  2.2975        -453.1855420  20.160  18.985   3.454  63.121
  13     -453.1855420 0.27199        -452.9135526 0.28467        -453.1982270  14.384  13.839   2.349  92.815
   7     -453.1982270 0.46650        -452.7317307 0.80814E-01    -452.8125449  16.146  15.160   2.254  96.721
  11     -452.8125449 0.78817        -452.0243793 0.76255        -452.7869308   1.828   1.647 145.148   1.502
   8     -452.7869308  2.3994        -450.3874814  2.2424        -452.6298675  30.812  29.198   2.456  88.762
  10     -452.6298675 0.10126        -452.5286058  1.7628        -454.2913664  15.578  14.524   3.327  65.520
   4     -454.2913664  6.0865        -448.2049057 0.61557        -448.8204776  41.657  32.216   1.714 127.163
   2     -448.8204776  2.9031        -445.9174065 0.72012        -446.6375222  66.246  62.118   1.879 116.011
   6     -446.6375222 0.20316        -446.4343597 0.17849        -446.6128535  26.493  25.719   1.823 119.565
   3     -446.6128535 0.55964E-01    -446.5568900 0.90170        -447.4585935  18.808  18.433   2.090 104.310
   5     -447.4585935  3.0986        -444.3600247  3.9770        -448.3370061   8.867   7.678  29.018   7.512
   9     -448.3370061 0.54727        -447.7897362 0.88611        -448.6758498   1.996   1.828  98.935   2.203

 Number of TS in the path       =     12
 Number of cycles               =      5

 Elapsed time=                              1350.61
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             88244 time=         663.68 %= 49.1
 OPTIM> # of energy+gradient+Hessian calls=      1006 time=         298.31 %= 22.1
