
 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 11:07:17
  [-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=    -529.9951317     RMS force=    0.8845597060E-06
 OPTIM> Final energy  =    -528.7933925     RMS force=    0.9762678435E-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=     8893.4    
 decide> The unconnected minima in the chain and their distances are:
     2       20.72     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 210 RMS= 0.9970 Dev= 1.89% S= 27.33 time= 2.52
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.95

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     632 steps. Energy=    -529.8722765       time=       1.59
 Minus side of path:                     665 steps. Energy=    -528.7933925       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765  2.6260         -527.2463100  1.5471         -528.7933925  14.946  13.186   5.314  20.137
        *NEW* (Placed in 3)                                     Known (#2)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     4184.2    
 decide> The unconnected minima in the chain and their distances are:
     3       16.11     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 1.1698 Dev= 1.23% S= 22.17 time= 1.12
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.22

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     607 steps. Energy=    -530.1820588       time=       1.49
 Minus side of path:                     596 steps. Energy=    -526.9228498       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1820588  3.5484         -526.6336108 0.28924         -526.9228498  11.302   9.984  10.176  10.515
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     3548.8    
 decide> The unconnected minima in the chain and their distances are:
     3        3.67     4     5       15.18     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0541 Dev= 0.09% S= 3.73 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   2.94

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     530 steps. Energy=    -529.8722765       time=       1.28
 Minus side of path:                     595 steps. Energy=    -530.1820588       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765 0.22853E-02     -529.8699912 0.31207         -530.1820588   3.759   3.667  15.894   6.732
        Known (#3)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.6698 Dev= 1.62% S= 18.75 time= 1.12
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     935 steps. Energy=    -529.8722765       time=       2.62
 Minus side of path:                     695 steps. Energy=    -529.4514373       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765  4.4803         -525.3919375  4.0595         -529.4514373  13.010   3.677   9.797  10.922
        *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      6 steps with      2 missing connections, weight=     2188.5    
 decide> The unconnected minima in the chain and their distances are:
     5        8.44     6     7       11.66     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3986 Dev= 0.35% S= 9.02 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     583 steps. Energy=    -528.5807680       time=       1.43
 Minus side of path:                     618 steps. Energy=    -529.6803965       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.5807680 0.10526E-01     -528.5702421  1.1102         -529.6803965   8.326   8.069   4.753  22.510
        *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 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 2.3205 Dev= 1.62% S= 13.47 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.86
 isnewts> transition state is the same as number        4 energy=     -525.3919374907
 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:                     922 steps. Energy=    -529.8722765       time=       2.58
 Minus side of path:                     688 steps. Energy=    -529.4514373       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765  4.4803         -525.3919375  4.0595         -529.4514373  13.021   3.699   9.581  11.168
        Known (#6)                                              Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     2593.9    
 decide> The unconnected minima in the chain and their distances are:
     5        7.77     8     8        4.13     6     6       12.71     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= 5.1283 Dev= 0.14% S= 7.99 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.31

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     725 steps. Energy=    -529.6803965       time=       1.84
 Minus side of path:                     529 steps. Energy=    -526.9228498       time=       1.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.6803965  2.7799         -526.9005028 0.22347E-01     -526.9228498  10.244   9.501   8.232  12.998
        Known (#9)                                              Known (#5)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2689 Dev= 0.51% S= 4.81 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.83
 isnewts> transition state is the same as number        5 energy=     -528.5702420960
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     621 steps. Energy=    -529.6803965       time=       1.53
 Minus side of path:                     583 steps. Energy=    -528.5807680       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.6803965  1.1102         -528.5702421 0.10526E-01     -528.5807680   8.326   8.069   4.752  22.516
        Known (#9)                                              Known (#8)
 Alternative path found between members of the F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 0.7677 Dev= 1.00% S= 15.26 time= 0.60
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.19

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     665 steps. Energy=    -529.8722765       time=       1.67
 Minus side of path:                     581 steps. Energy=    -530.0277218       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765  2.1725         -527.6997698  2.3280         -530.0277218  14.505  11.983  16.728   6.397
        Known (#6)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     192.08    
 decide> The unconnected minima in the chain and their distances are:
     8        4.96     7    10        4.12     1 
 

 tryconnect> 70-iteration DNEB run for minima 7_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5616 Dev= 0.86% S= 5.56 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   4.31
 isnewts> transition state is the same as number        5 energy=     -528.5702420960
 tryconnect> Will not repeat search for TS      1 same as TS      5

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1153 Dev= 0.07% S= 4.29 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.34

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     554 steps. Energy=    -529.9951317       time=       1.34
 Minus side of path:                     568 steps. Energy=    -530.0277218       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.9951317 0.40820E-01     -529.9543112 0.73411E-01     -530.0277218   4.309   4.122  16.562   6.461
        Known (#1)                                              Known (#10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     140.71    
 decide> The unconnected minima in the chain and their distances are:
     8        4.13     6 
 

 tryconnect> 315-iteration DNEB run for minima 6_S and 8_F using 9 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 315 RMS= 0.0609 Dev= 5.62% S= 5.60 time= 5.72
 Following    2 images are candidates for TS:    5    9  
 Converged to TS (number of iterations):         12
 Converged to TS (number of iterations):         15
 DNEB run yielded 2 true transition state(s) time=   5.05
 isnewts> transition state is the same as number        5 energy=     -528.5702420960
 tryconnect> Will not repeat search for TS      2 same as TS      5

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     632 steps. Energy=    -529.8722765       time=       1.60
 Minus side of path:                     597 steps. Energy=    -529.6803965       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765  8.3669         -521.5054170  8.1750         -529.6803965   6.396   5.891  12.472   8.579
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -529.9951317 0.40820E-01    -529.9543112 0.73411E-01    -530.0277218   4.309   4.122  16.562   6.461
   9     -530.0277218  2.3280        -527.6997698  2.1725        -529.8722765  14.505  11.983  16.728   6.397
  11     -529.8722765  8.3669        -521.5054170  8.1750        -529.6803965   6.396   5.891  12.472   8.579
   7     -529.6803965  2.7799        -526.9005028 0.22347E-01    -526.9228498  10.244   9.501   8.232  12.998
   2     -526.9228498 0.28924        -526.6336108  3.5484        -530.1820588  11.302   9.984  10.176  10.515
   3     -530.1820588 0.31207        -529.8699912 0.22853E-02    -529.8722765   3.759   3.667  15.894   6.732
   1     -529.8722765  2.6260        -527.2463100  1.5471        -528.7933925  14.946  13.186   5.314  20.137

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

 Elapsed time=                               104.69
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             29149 time=          58.54 %= 55.9
 OPTIM> # of energy+gradient+Hessian calls=       462 time=          24.96 %= 23.8
