
 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 21:30:59
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -446.6425488     RMS force=    0.9861316752E-06
 OPTIM> Final energy  =    -449.0251467     RMS force=    0.9925072808E-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=     14196.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.21     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= 0.2200 Dev= 1.96% S= 40.90 time= 12.93
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 143.60
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     28392.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.21     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3317813797E-01
 Double-ended search iterations= 805 RMS= 0.0358 Dev= 5.01% S= 67.73 time= 138.84
 Following    3 images are candidates for TS:    1    5   16  
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         49
 Converged to TS (number of iterations):         86
 DNEB run yielded 3 true transition state(s) time= 138.08

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1384 steps. Energy=    -447.3016277       time=      19.77
 Minus side of path:                    1286 steps. Energy=    -446.6425488       time=      18.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3016277 0.66281         -446.6388217 0.37270E-02     -446.6425488  18.626  18.315   3.132  69.597
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1358 steps. Energy=    -446.8657111       time=      15.56
 Minus side of path:                    1388 steps. Energy=    -447.9185244       time=      16.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8657111  1.5569         -445.3088368  2.6097         -447.9185244  33.267  24.541   4.494  48.512
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1322 steps. Energy=    -445.8415769       time=      16.24
 Minus side of path:                    1350 steps. Energy=    -446.3179935       time=      18.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.8415769  1.5287         -444.3128744  2.0051         -446.3179935  34.963  20.787  18.299  11.913
        *NEW* (Placed in 6)                                     *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      2 steps with      1 missing connections, weight=     3437.4    
 decide> The unconnected minima in the chain and their distances are:
     2       15.09     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4795 Dev= 1.02% S= 30.09 time= 4.54
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=  53.19
 isnewts> transition state is the same as number        2 energy=     -445.3088368002
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1355 steps. Energy=    -446.8657111       time=      17.52
 Minus side of path:                    1376 steps. Energy=    -447.9185244       time=      17.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8657111  1.5569         -445.3088368  2.6097         -447.9185244  33.268  24.542   4.494  48.514
        Known (#4)                                              Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6874.7    
 decide> The unconnected minima in the chain and their distances are:
     2       15.09     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 805 RMS= 0.0411 Dev= 6.64% S= 54.73 time= 138.07
 Following    2 images are candidates for TS:    9   20  
 Converged to TS (number of iterations):        131
 Converged to TS (number of iterations):         30
 DNEB run yielded 2 true transition state(s) time= 104.49
 isnewts> transition state is the same as number        2 energy=     -445.3088368013
 tryconnect> Will not repeat search for TS      2 same as TS      2

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1473 steps. Energy=    -449.0251467       time=      16.55
 Minus side of path:                    1343 steps. Energy=    -448.3428856       time=      15.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0251467  2.3728         -446.6523922  1.6905         -448.3428856  49.369  27.479   1.760 123.870
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     9904.5    
 decide> The unconnected minima in the chain and their distances are:
     2       18.02     4     5       15.95     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 0.4713 Dev= 1.81% S= 25.37 time= 6.57
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  54.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1430 steps. Energy=    -446.3179936       time=      18.59
 Minus side of path:                    1338 steps. Energy=    -445.8415769       time=      16.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.3179936  3.8167         -442.5012785  3.3403         -445.8415769  31.395  20.776  19.377  11.251
        Known (#7)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 3_S and 5_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0347 Dev= 0.06% S= 16.07 time= 4.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=  49.57

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1327 steps. Energy=    -447.9185244       time=      14.12
 Minus side of path:                    1306 steps. Energy=    -447.3016277       time=      13.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.9185244 0.63292         -447.2856058 0.16022E-01     -447.3016277  16.186  15.954   4.528  48.146
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     7923.2    
 decide> The unconnected minima in the chain and their distances are:
     2       19.94     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2567 Dev= 0.33% S= 33.79 time= 6.72
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=  63.11

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1388 steps. Energy=    -446.8975280       time=      15.46
 Minus side of path:                    1381 steps. Energy=    -446.8657111       time=      15.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8975280  1.7270         -445.1705585  1.6952         -446.8657111  40.336  34.147   3.392  64.260
        *NEW* (Placed in 9)                                     Known (#4)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3697.2    
 decide> The unconnected minima in the chain and their distances are:
     8       15.46     9 
 

 tryconnect> 140-iteration DNEB run for minima 8_F and 9_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.4214 Dev= 1.22% S= 21.15 time= 4.39
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=  38.29

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1343 steps. Energy=    -446.7061821       time=      16.25
 Minus side of path:                    1449 steps. Energy=    -448.3428856       time=      18.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.7061821  3.4754         -443.2308259  5.1121         -448.3428856  36.669  20.020  25.034   8.708
        *NEW* (Placed in 10)                                    Known (#8)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     2660.8    
 decide> The unconnected minima in the chain and their distances are:
    10       13.86     9 
 

 tryconnect> 140-iteration DNEB run for minima 9_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1273 Dev= 0.01% S= 13.92 time= 4.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  34.12

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1312 steps. Energy=    -446.8975280       time=      16.86
 Minus side of path:                    1269 steps. Energy=    -446.7061821       time=      15.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8975280 0.22736         -446.6701632 0.36019E-01     -446.7061821  15.547  13.863   6.702  32.530
        Known (#9)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -446.6425488 0.37270E-02    -446.6388217 0.66281        -447.3016277  18.626  18.315   3.132  69.597
   7     -447.3016277 0.16022E-01    -447.2856058 0.63292        -447.9185244  16.186  15.954   4.528  48.146
   2     -447.9185244  2.6097        -445.3088368  1.5569        -446.8657111  33.267  24.541   4.494  48.512
   8     -446.8657111  1.6952        -445.1705585  1.7270        -446.8975280  40.336  34.147   3.392  64.260
  10     -446.8975280 0.22736        -446.6701632 0.36019E-01    -446.7061821  15.547  13.863   6.702  32.530
   9     -446.7061821  3.4754        -443.2308259  5.1121        -448.3428856  36.669  20.020  25.034   8.708
   5     -448.3428856  1.6905        -446.6523922  2.3728        -449.0251467  49.369  27.479   1.760 123.870

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

 Elapsed time=                              1333.73
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             89002 time=         662.19 %= 49.6
 OPTIM> # of energy+gradient+Hessian calls=      1006 time=         291.26 %= 21.8
