
 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 09:39:53
  [-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=    -537.3192863     RMS force=    0.8441283797E-06
 OPTIM> Final energy  =    -538.9508357     RMS force=    0.8038790269E-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=     6856.7    
 decide> The unconnected minima in the chain and their distances are:
     2       19.00     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.4517 Dev= 2.36% S= 25.02 time= 1.75
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   7.27

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     596 steps. Energy=    -539.4563928       time=       1.46
 Minus side of path:                     598 steps. Energy=    -540.5611630       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -539.4563928 0.23585         -539.2205445  1.3406         -540.5611630   6.723   5.705  18.861   5.673
        *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      3 steps with      2 missing connections, weight=     4709.8    
 decide> The unconnected minima in the chain and their distances are:
     2       10.77     4     3       15.13     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 1.3799 Dev= 2.03% S= 14.92 time= 0.62
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.03

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     559 steps. Energy=    -538.9508357       time=       1.36
 Minus side of path:                     582 steps. Energy=    -540.5189575       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.9508357 0.11100         -538.8398352  1.6791         -540.5189575   4.482   4.420   5.023  21.304
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 1.4148 Dev= 1.02% S= 17.77 time= 1.13
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  25.31
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     5176.1    
 decide> The unconnected minima in the chain and their distances are:
     5       10.05     4     4       16.08     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 1.2677 Dev= 2.13% S= 15.37 time= 0.50
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.32

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     624 steps. Energy=    -540.5611630       time=       1.54
 Minus side of path:                     634 steps. Energy=    -540.5189575       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.5611630  4.8610         -535.7001933  4.8188         -540.5189575  15.681  10.243  14.942   7.161
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.6824 Dev= 1.53% S= 18.73 time= 1.13
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  23.47
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6417.8    
 decide> The unconnected minima in the chain and their distances are:
     5       18.58     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 175 RMS= 0.6769 Dev= 1.79% S= 24.30 time= 1.64
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        133
 DNEB run yielded 1 true transition state(s) time=  12.68

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     534 steps. Energy=    -539.3031557       time=       1.29
 Minus side of path:                     643 steps. Energy=    -540.4032007       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -539.3031557 0.63236         -538.6708004  1.7324         -540.4032007  16.644  15.403   3.819  28.018
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     5426.4    
 decide> The unconnected minima in the chain and their distances are:
     2       10.90     7     7       16.05     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.9536 Dev= 0.29% S= 12.30 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.55

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     653 steps. Energy=    -540.4032007       time=       1.62
 Minus side of path:                     559 steps. Energy=    -541.2713978       time=       1.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.4032007  3.4944         -536.9088020  4.3626         -541.2713978  13.637   9.566   2.460  43.494
        Known (#7)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 140 RMS= 0.6240 Dev= 0.88% S= 19.66 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        218
 DNEB run yielded 1 true transition state(s) time=  21.97

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     620 steps. Energy=    -540.4032007       time=       1.55
 Minus side of path:                     584 steps. Energy=    -539.4887563       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.4032007 0.92820         -539.4750056 0.13751E-01     -539.4887563   6.498   6.447   2.892  36.996
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     3776.8    
 decide> The unconnected minima in the chain and their distances are:
     5        8.50     8     7        9.91     9     9       12.98     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3266 Dev= 0.04% S= 8.68 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     549 steps. Energy=    -540.5189575       time=       1.35
 Minus side of path:                     597 steps. Energy=    -541.2713978       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.5189575 0.13469         -540.3842692 0.88713         -541.2713978   8.966   8.502   7.941  13.475
        Known (#5)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.

 checkpair> Energies of the minima in the pair     7    9 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 5.3821 Dev= 2.67% S= 14.18 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.67

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     604 steps. Energy=    -540.6705277       time=       1.49
 Minus side of path:                     600 steps. Energy=    -540.4032007       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.6705277  8.7260         -531.9444995  8.4587         -540.4032007   2.843   1.689  60.278   1.775
        *NEW* (Placed in 11)                                    Known (#7)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0972 Dev= 0.04% S= 13.25 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     592 steps. Energy=    -537.3192863       time=       1.46
 Minus side of path:                     841 steps. Energy=    -540.4032007       time=       2.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.3192863 0.11742         -537.2018633  3.2013         -540.4032007  14.446  12.994   4.200  25.474
        Known (#1)                                              Known (#9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1014.2    
 decide> The unconnected minima in the chain and their distances are:
    11       10.05     9 
 

 tryconnect> 105-iteration DNEB run for minima 9_S and 11_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 1.2470 Dev= 0.76% S= 15.25 time= 0.56
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.01

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     637 steps. Energy=    -540.4032007       time=       1.57
 Minus side of path:                     626 steps. Energy=    -540.6705277       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -540.4032007  3.2777         -537.1255135  3.5450         -540.6705277  14.703  10.149  15.453   6.924
        Known (#9)                                              Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -537.3192863 0.11742        -537.2018633  3.2013        -540.4032007  14.446  12.994   4.200  25.474
  10     -540.4032007  3.2777        -537.1255135  3.5450        -540.6705277  14.703  10.149  15.453   6.924
   8     -540.6705277  8.7260        -531.9444995  8.4587        -540.4032007   2.843   1.689  60.278   1.775
   5     -540.4032007  3.4944        -536.9088020  4.3626        -541.2713978  13.637   9.566   2.460  43.494
   7     -541.2713978 0.88713        -540.3842692 0.13469        -540.5189575   8.966   8.502   7.941  13.475
   2     -540.5189575  1.6791        -538.8398352 0.11100        -538.9508357   4.482   4.420   5.023  21.304

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               164.84
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             28386 time=          57.12 %= 34.7
 OPTIM> # of energy+gradient+Hessian calls=      1221 time=          66.10 %= 40.1
