
 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 05/28/2012 at 09:33:26
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -534.4949160     RMS force=    0.9419527403E-06
 OPTIM> Final energy  =    -534.0955396     RMS force=    0.8208331121E-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=     4112.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.02     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 1.2982 Dev= 1.03% S= 21.43 time= 1.12
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   9.38

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     645 steps. Energy=    -533.9658437       time=       1.57
 Minus side of path:                     676 steps. Energy=    -533.9604048       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9658437  2.7180         -531.2478056  2.7126         -533.9604048  16.393  10.170  15.414   6.942
        *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=     8224.5    
 decide> The unconnected minima in the chain and their distances are:
     2       16.02     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 805 RMS= 0.7501 Dev= 5.54% S= 25.82 time= 36.64
 Following    3 images are candidates for TS:    6   15   18  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         91
 Converged to TS (number of iterations):         57
 DNEB run yielded 3 true transition state(s) time=  18.99
 isnewts> transition state is the same as number        1 energy=     -531.2478056118
 tryconnect> Try the path again for ts      3 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     609 steps. Energy=    -534.4949160       time=       1.48
 Minus side of path:                     613 steps. Energy=    -535.2494145       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4949160  3.1937         -531.3011755  3.9482         -535.2494145   8.175   7.233   8.672  12.339
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     643 steps. Energy=    -534.6554246       time=       1.59
 Minus side of path:                     627 steps. Energy=    -533.9604048       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6554246 0.81102         -533.8444055 0.11600         -533.9604048   6.548   5.620  28.244   3.788
        *NEW* (Placed in 6)                                     Known (#4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     660 steps. Energy=    -533.9604048       time=       1.64
 Minus side of path:                     642 steps. Energy=    -533.9658437       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9604048  2.7126         -531.2478056  2.7180         -533.9658437  16.394  10.174  15.392   6.951
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2811.4    
 decide> The unconnected minima in the chain and their distances are:
     2       14.11     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 1.0755 Dev= 0.83% S= 19.22 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        127
 DNEB run yielded 1 true transition state(s) time=  13.45

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     596 steps. Energy=    -533.7032948       time=       1.43
 Minus side of path:                     638 steps. Energy=    -534.5186025       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7032948 0.19860E-01     -533.6834349 0.83517         -534.5186025   5.999   5.835   4.539  23.571
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     3498.2    
 decide> The unconnected minima in the chain and their distances are:
     2        8.25     7     7       14.32     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3130 Dev= 0.18% S= 8.61 time= 0.28
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.27
 isnewts> transition state is the same as number        5 energy=     -533.6834348731
 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:                     610 steps. Energy=    -533.7032948       time=       1.48
 Minus side of path:                     646 steps. Energy=    -534.5186025       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7032948 0.19860E-01     -533.6834349 0.83517         -534.5186025   5.998   5.835   4.536  23.587
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 5_S and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 1.1270 Dev= 1.04% S= 19.87 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.47
 isnewts> transition state is the same as number        1 energy=     -531.2478056117
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     4874.4    
 decide> The unconnected minima in the chain and their distances are:
     2        8.25     7     8       15.54     5 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 7_U using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 630 RMS= 0.0231 Dev= 5.83% S= 11.69 time= 22.78
 Following    2 images are candidates for TS:    2   10  
 Converged to TS (number of iterations):          6
 Converged to TS (number of iterations):         18
 DNEB run yielded 2 true transition state(s) time=   4.58

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     623 steps. Energy=    -534.6241129       time=       1.52
 Minus side of path:                     556 steps. Energy=    -534.0955396       time=       1.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129 0.53760         -534.0865145 0.90251E-02     -534.0955396   8.970   8.867   4.908  21.803
        *NEW* (Placed in 9)                                     Known (#2)
 Unconnected minimum 9 found its way to F set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     637 steps. Energy=    -534.5186025       time=       1.58
 Minus side of path:                     604 steps. Energy=    -534.6241129       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5186025  8.5878         -525.9308383  8.6933         -534.6241129   6.141   2.486  57.975   1.846
        Known (#8)                                              Known (#9)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 5_S and 8_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 140 RMS= 0.5417 Dev= 0.67% S= 20.52 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.54
 isnewts> transition state is the same as number        1 energy=     -531.2478056118
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3269.4    
 decide> The unconnected minima in the chain and their distances are:
     9       14.84     5 
 

 tryconnect> 140-iteration DNEB run for minima 5_S and 9_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.7901 Dev= 0.90% S= 20.24 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.68

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     681 steps. Energy=    -534.5186025       time=       1.67
 Minus side of path:                     678 steps. Energy=    -534.6241129       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5186025  4.6096         -529.9089815  4.7151         -534.6241129  22.638  10.431  13.976   7.656
        *NEW* (Placed in 10)                                    Known (#9)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1780.2    
 decide> The unconnected minima in the chain and their distances are:
    10       12.12     5 
 

 tryconnect> 105-iteration DNEB run for minima 5_S and 10_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3442 Dev= 0.15% S= 13.71 time= 0.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.22

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     613 steps. Energy=    -535.2494145       time=       1.48
 Minus side of path:                     650 steps. Energy=    -534.6241129       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2494145  1.3654         -533.8840039 0.74011         -534.6241129  14.145  11.232   9.050  11.823
        Known (#5)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     15.352    
 decide> The unconnected minima in the chain and their distances are:
    10        2.49    11 
 

 tryconnect> 70-iteration DNEB run for minima 10_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.7297 Dev= 0.92% S= 3.06 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.45

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     601 steps. Energy=    -534.5186025       time=       1.45
 Minus side of path:                     640 steps. Energy=    -534.8131899       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5186025 0.21633         -534.3022710 0.51092         -534.8131899  11.872  11.197   5.164  20.719
        Known (#10)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     30.704    
 decide> The unconnected minima in the chain and their distances are:
    10        2.49    11 
 

 tryconnect> 175-iteration DNEB run for minima 10_F and 11_S using 5 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 175 RMS= 0.3828 Dev= 8.31% S= 3.41 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.55

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     648 steps. Energy=    -534.8131899       time=       1.59
 Minus side of path:                     612 steps. Energy=    -534.6241129       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.8131899  8.6969         -526.1163297  8.5078         -534.6241129  10.514   9.546   5.091  21.019
        Known (#12)                                             Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -534.4949160  3.1937        -531.3011755  3.9482        -535.2494145   8.175   7.233   8.672  12.339
  10     -535.2494145  1.3654        -533.8840039 0.74011        -534.6241129  14.145  11.232   9.050  11.823
  12     -534.6241129  8.5078        -526.1163297  8.6969        -534.8131899  10.514   9.546   5.091  21.019
  11     -534.8131899 0.51092        -534.3022710 0.21633        -534.5186025  11.872  11.197   5.164  20.719
   9     -534.5186025  4.6096        -529.9089815  4.7151        -534.6241129  22.638  10.431  13.976   7.656
   7     -534.6241129 0.53760        -534.0865145 0.90251E-02    -534.0955396   8.970   8.867   4.908  21.803

 Number of TS in the path       =      6
 Number of cycles               =      9

 Elapsed time=                               189.67
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             60093 time=         118.63 %= 62.5
 OPTIM> # of energy+gradient+Hessian calls=       755 time=          40.45 %= 21.3
