
 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 20:22:28
  [-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=    -447.3249508     RMS force=    0.9550050346E-06
 OPTIM> Final energy  =    -448.0341921     RMS force=    0.8557139743E-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=     16168.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.29     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 245 RMS= 0.1180 Dev= 0.23% S= 27.61 time= 12.75
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=  39.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1445 steps. Energy=    -453.6281855       time=      16.57
 Minus side of path:                    1260 steps. Energy=    -452.3275124       time=      13.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6281855  7.9661         -445.6620662  6.6654         -452.3275124  40.796  32.508   1.852 117.712
        *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      1 steps with      1 missing connections, weight=     32335.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.29     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 805 RMS= 0.0457 Dev= 5.98% S= 33.36 time= 137.43
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  31.87
 isnewts> transition state is the same as number        1 energy=     -445.6620662446
 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:                    1449 steps. Energy=    -453.6281855       time=      15.78
 Minus side of path:                    1270 steps. Energy=    -452.3275124       time=      13.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6281855  7.9661         -445.6620662  6.6654         -452.3275124  40.797  32.504   1.852 117.731
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     66418.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.21     4     4       26.66     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0562 Dev= 1.70% S= 39.26 time= 26.00
 Following    2 images are candidates for TS:    4    6  
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):        172
 DNEB run yielded 2 true transition state(s) time= 125.90
 isnewts> transition state is the same as number        3 energy=     -447.4086614543
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1788 steps. Energy=    -452.7896986       time=      21.41
 Minus side of path:                    1520 steps. Energy=    -448.0341921       time=      16.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.7896986  5.3810         -447.4086615 0.62553         -448.0341921  46.139  36.733   2.382  91.506
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1737 steps. Energy=    -452.7896986       time=      20.49
 Minus side of path:                    1514 steps. Energy=    -448.0341921       time=      16.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.7896986  5.3810         -447.4086615 0.62553         -448.0341921  46.146  36.743   2.383  91.474
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 245 RMS= 0.6238 Dev= 0.78% S= 29.24 time= 12.73
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=  35.35

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1453 steps. Energy=    -453.6281855       time=      15.94
 Minus side of path:                    1259 steps. Energy=    -452.3275124       time=      13.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6281855  8.0158         -445.6124062  6.7151         -452.3275124  40.270  32.503   1.852 117.683
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     21453.    
 decide> The unconnected minima in the chain and their distances are:
     5       27.79     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 5_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 280 RMS= 0.0950 Dev= 0.42% S= 30.72 time= 16.67
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  30.28

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1588 steps. Energy=    -453.8915902       time=      19.79
 Minus side of path:                    1212 steps. Energy=    -452.7896986       time=      12.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8915902  7.8721         -446.0194949  6.7702         -452.7896986  45.338  36.995   1.833 118.940
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     33485.    
 decide> The unconnected minima in the chain and their distances are:
     5        7.02     4     3       32.12     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0676 Dev= 0.01% S= 7.06 time= 1.06
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  24.52

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1104 steps. Energy=    -452.3006484       time=      11.51
 Minus side of path:                    1199 steps. Energy=    -452.7896986       time=      12.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.3006484 0.14422E-02     -452.2992062 0.49049         -452.7896986   5.951   5.433  13.351  16.329
        *NEW* (Placed in 7)                                     Known (#5)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 3_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1631 Dev= 2.61% S= 35.08 time= 21.12
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=  46.33

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1310 steps. Energy=    -447.3249508       time=      15.70
 Minus side of path:                    1649 steps. Energy=    -450.2514732       time=      20.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3249508 0.24694         -447.0780100  3.1735         -450.2514732  33.777  29.207   2.640  82.572
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     18638.    
 decide> The unconnected minima in the chain and their distances are:
     7       26.51     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 245 RMS= 0.1856 Dev= 0.60% S= 29.23 time= 12.74
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=  35.16
 isnewts> transition state is the same as number        5 energy=     -445.6124062488
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1455 steps. Energy=    -453.6281855       time=      17.00
 Minus side of path:                    1267 steps. Energy=    -452.3275124       time=      14.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6281855  8.0158         -445.6124062  6.7151         -452.3275124  40.270  32.499   1.852 117.695
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     35355.    
 decide> The unconnected minima in the chain and their distances are:
     7        2.51     4     3       32.82     8 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0125 Dev= 0.00% S= 2.51 time= 1.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=  16.70

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1092 steps. Energy=    -452.3006483       time=      10.73
 Minus side of path:                    1203 steps. Energy=    -452.3275124       time=      12.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.3006483 0.12941E-01     -452.2877078 0.39805E-01     -452.3275124   2.515   2.508   4.787  45.537
        Known (#7)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 3_F and 8_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0719 Dev= 2.01% S= 36.34 time= 21.11
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        159
 DNEB run yielded 1 true transition state(s) time=  82.68

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1268 steps. Energy=    -450.2514732       time=      13.24
 Minus side of path:                    1349 steps. Energy=    -451.1954980       time=      14.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2514732 0.13619         -450.1152791  1.0802         -451.1954980  32.196  29.984   2.121 102.759
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 9 minima and 11 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     9417.2    
 decide> The unconnected minima in the chain and their distances are:
     3       21.12     9 
 

 tryconnect> 210-iteration DNEB run for minima 3_F and 9_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0472 Dev= 0.29% S= 21.41 time= 9.47
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=  41.37

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1261 steps. Energy=    -451.1954980       time=      13.33
 Minus side of path:                    1275 steps. Energy=    -453.6281855       time=      13.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.1954980 0.20921         -450.9862837  2.6419         -453.6281855  22.342  21.124   4.352  50.088
        Known (#9)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -447.3249508 0.24694        -447.0780100  3.1735        -450.2514732  33.777  29.207   2.640  82.572
  11     -450.2514732 0.13619        -450.1152791  1.0802        -451.1954980  32.196  29.984   2.121 102.759
  12     -451.1954980 0.20921        -450.9862837  2.6419        -453.6281855  22.342  21.124   4.352  50.088
   1     -453.6281855  7.9661        -445.6620662  6.6654        -452.3275124  40.796  32.508   1.852 117.712
  10     -452.3275124 0.39805E-01    -452.2877078 0.12941E-01    -452.3006484   2.515   2.508   4.787  45.537
   7     -452.3006484 0.14422E-02    -452.2992062 0.49049        -452.7896986   5.951   5.433  13.351  16.329
   3     -452.7896986  5.3810        -447.4086615 0.62553        -448.0341921  46.139  36.733   2.382  91.506

 Number of TS in the path       =      7
 Number of cycles               =      8

 Elapsed time=                              1148.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             86735 time=         640.79 %= 55.8
 OPTIM> # of energy+gradient+Hessian calls=       793 time=         219.96 %= 19.1
