
 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 09:34:40
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -531.4254363     RMS force=    0.9187352584E-06
 OPTIM> Final energy  =    -533.4937306     RMS force=    0.8869974862E-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=     2351.5    
 decide> The unconnected minima in the chain and their distances are:
     2       13.30     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 6.0130 Dev= 0.20% S= 18.77 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     645 steps. Energy=    -532.1197665       time=       1.59
 Minus side of path:                     653 steps. Energy=    -532.1227132       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665  2.7124         -529.4073688  2.7153         -532.1227132  16.683  10.168  15.434   6.933
        *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=     4703.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.30     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 805 RMS= 0.2779 Dev= 5.95% S= 23.42 time= 37.54
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   7.52
 isnewts> transition state is the same as number        1 energy=     -529.4073688272
 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:                     648 steps. Energy=    -532.1227132       time=       1.60
 Minus side of path:                     632 steps. Energy=    -532.1197665       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1227132  2.7153         -529.4073688  2.7124         -532.1197665  16.690  10.186  15.329   6.980
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     7159.6    
 decide> The unconnected minima in the chain and their distances are:
     2       15.80     3     4       14.75     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.8974 Dev= 0.37% S= 16.65 time= 1.26
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     607 steps. Energy=    -532.1197665       time=       1.47
 Minus side of path:                     615 steps. Energy=    -532.6820344       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665 0.34157E-01     -532.0856099 0.59642         -532.6820344   2.800   2.692  34.747   3.079
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0968 Dev= 0.09% S= 15.29 time= 1.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        144
 DNEB run yielded 1 true transition state(s) time=  14.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     787 steps. Energy=    -533.5516165       time=       2.03
 Minus side of path:                     565 steps. Energy=    -531.8903757       time=       1.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5516165  2.5053         -531.0463079 0.84407         -531.8903757  19.912  16.815   3.280  32.627
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 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      2 missing connections, weight=     2236.3    
 decide> The unconnected minima in the chain and their distances are:
     2       10.71     6     6       10.03     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 4.2139 Dev= 0.64% S= 17.02 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   6.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     638 steps. Energy=    -532.8944176       time=       1.57
 Minus side of path:                     646 steps. Energy=    -532.8977811       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.8944176  2.7174         -530.1769714  2.7208         -532.8977811  16.659  10.173  15.403   6.947
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2072 Dev= 0.69% S= 11.74 time= 0.74
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.48

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     671 steps. Energy=    -533.4937306       time=       1.65
 Minus side of path:                     547 steps. Energy=    -531.4254363       time=       1.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4937306  2.1192         -531.3745174 0.50919E-01     -531.4254363  10.402   9.486  10.330  10.358
        *NEW* (Placed in 10)                                    Known (#1)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     974.56    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91    10 
 

 checkpair> Energies of the minima in the pair     2   10 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.2784 Dev= 1.24% S= 15.36 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.07

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     661 steps. Energy=    -533.4937306       time=       1.62
 Minus side of path:                     592 steps. Energy=    -532.5989921       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4937306  4.5768         -528.9169055  3.6821         -532.5989921  15.523  12.618   7.442  14.377
        Known (#10)                                             *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     869.02    
 decide> The unconnected minima in the chain and their distances are:
     2        9.54    11 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8027 Dev= 0.22% S= 9.95 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.38

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     539 steps. Energy=    -532.5989921       time=       1.31
 Minus side of path:                     688 steps. Energy=    -532.7976427       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5989921 0.10677         -532.4922184 0.30542         -532.7976427   8.539   7.493   2.708  39.519
        Known (#11)                                             *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     139.80    
 decide> The unconnected minima in the chain and their distances are:
     2        5.19    12 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2561 Dev= 0.69% S= 5.71 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   8.50

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     761 steps. Energy=    -533.7374985       time=       1.94
 Minus side of path:                     661 steps. Energy=    -533.1362820       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7374985  1.7351         -532.0024439  1.1338         -533.1362820  13.339  12.339   3.482  30.731
        *NEW* (Placed in 13)                                    *NEW* (Placed in 14)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     279.60    
 decide> The unconnected minima in the chain and their distances are:
     2        5.19    12 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 12_S using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 385 RMS= 0.0272 Dev= 3.49% S= 7.01 time= 8.63
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.17

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     569 steps. Energy=    -533.4937306       time=       1.36
 Minus side of path:                     631 steps. Energy=    -532.7976427       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4937306  8.7988         -524.6949108  8.1027         -532.7976427   5.628   5.191  15.532   6.889
        Known (#2)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -531.4254363 0.50919E-01    -531.3745174  2.1192        -533.4937306  10.402   9.486  10.330  10.358
   7     -533.4937306  4.5768        -528.9169055  3.6821        -532.5989921  15.523  12.618   7.442  14.377
   8     -532.5989921 0.10677        -532.4922184 0.30542        -532.7976427   8.539   7.493   2.708  39.519
  10     -532.7976427  8.1027        -524.6949108  8.7988        -533.4937306   5.628   5.191  15.532   6.889

 Number of TS in the path       =      4
 Number of cycles               =      8

 Elapsed time=                               148.12
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45473 time=          90.52 %= 61.1
 OPTIM> # of energy+gradient+Hessian calls=       606 time=          32.54 %= 22.0
