
 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 10:40:58
  [-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=    -531.6775152     RMS force=    0.9183732701E-06
 OPTIM> Final energy  =    -535.7097230     RMS force=    0.9916757157E-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=     26603.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.85     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 280 RMS= 0.8965 Dev= 2.18% S= 36.33 time= 4.42
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=   7.62

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     684 steps. Energy=    -536.7268830       time=       1.72
 Minus side of path:                     817 steps. Energy=    -532.6416259       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.7268830  5.3028         -531.4241269  1.2175         -532.6416259  23.835  19.468   2.615  40.916
        *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=     13383.    
 decide> The unconnected minima in the chain and their distances are:
     2       13.41     3     4       22.22     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= 0.1736 Dev= 0.32% S= 14.58 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     632 steps. Energy=    -535.7097230       time=       1.57
 Minus side of path:                     645 steps. Energy=    -537.0052404       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.7097230  3.2943         -532.4153899  4.5899         -537.0052404  15.397  12.118   5.025  21.295
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 210 RMS= 0.5927 Dev= 0.87% S= 24.72 time= 2.53
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        190
 DNEB run yielded 1 true transition state(s) time=  17.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     738 steps. Energy=    -532.6416259       time=       1.89
 Minus side of path:                     617 steps. Energy=    -532.2781679       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6416259 0.43757         -532.2040523 0.74116E-01     -532.2781679  11.486  10.063   2.845  37.606
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     10066.    
 decide> The unconnected minima in the chain and their distances are:
     5        4.96     3     6       21.50     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0832 Dev= 0.11% S= 5.11 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.71

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     589 steps. Energy=    -537.0052404       time=       1.44
 Minus side of path:                     598 steps. Energy=    -536.7268830       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.0052404 0.36596         -536.6392811 0.87602E-01     -536.7268830   6.181   4.966  20.838   5.135
        Known (#5)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1112 Dev= 0.53% S= 22.94 time= 2.54
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   8.21

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     539 steps. Energy=    -535.0935480       time=       1.30
 Minus side of path:                     638 steps. Energy=    -535.6041211       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.0935480 0.49219E-01     -535.0443292 0.55979         -535.6041211   4.608   4.444   4.370  24.485
        *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      6 steps with      2 missing connections, weight=     9769.2    
 decide> The unconnected minima in the chain and their distances are:
     6       11.65     8     8       20.16     1 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2513 Dev= 0.12% S= 12.48 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.31

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     576 steps. Energy=    -532.2781679       time=       1.41
 Minus side of path:                     605 steps. Energy=    -533.9861067       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2781679 0.29901         -531.9791570  2.0069         -533.9861067  10.903  10.235   6.324  16.919
        Known (#6)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 8_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1192 Dev= 0.29% S= 20.66 time= 2.55
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=   8.89
 isnewts> transition state is the same as number        5 energy=     -535.0443291977
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     553 steps. Energy=    -535.0935480       time=       1.34
 Minus side of path:                     642 steps. Energy=    -535.6041211       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.0935480 0.49219E-01     -535.0443292 0.55979         -535.6041211   4.608   4.444   4.368  24.499
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5582.2    
 decide> The unconnected minima in the chain and their distances are:
     9       17.74     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 9_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1208 Dev= 0.52% S= 18.43 time= 1.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   8.77
 isnewts> transition state is the same as number        5 energy=     -535.0443291977
 tryconnect> Will not repeat search for TS      1 same as TS      5
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     9281.9    
 decide> The unconnected minima in the chain and their distances are:
     9        4.53     8     7       20.95     1 
 

 tryconnect> 70-iteration DNEB run for minima 8_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5007 Dev= 0.80% S= 5.09 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=   9.84

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     593 steps. Energy=    -533.0698040       time=       1.45
 Minus side of path:                     663 steps. Energy=    -533.9861067       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0698040 0.42707         -532.6427319  1.3434         -533.9861067  16.712  16.035   3.194  33.497
        *NEW* (Placed in 10)                                    Known (#9)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 7_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0517 Dev= 0.12% S= 21.38 time= 2.54
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  22.12
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     2637.1    
 decide> The unconnected minima in the chain and their distances are:
    10       13.82     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 10_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 1.3332 Dev= 0.74% S= 14.66 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.25

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     626 steps. Energy=    -533.1302599       time=       1.56
 Minus side of path:                     614 steps. Energy=    -532.2918180       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1302599  1.1781         -531.9521953 0.33962         -532.2918180  11.168   9.800   1.833  58.385
        *NEW* (Placed in 11)                                    *NEW* (Placed in 12)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     1018.2    
 decide> The unconnected minima in the chain and their distances are:
    10        1.67    11    12       10.05     1 
 

 tryconnect> 70-iteration DNEB run for minima 10_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.3163 Dev= 0.96% S= 2.23 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=   2.56

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     602 steps. Energy=    -533.1302599       time=       1.48
 Minus side of path:                     596 steps. Energy=    -533.0698040       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1302599  8.6262         -524.5040647  8.5657         -533.0698040   2.806   1.666  84.469   1.267
        Known (#11)                                             Known (#10)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 12_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1207 Dev= 0.13% S= 10.33 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     665 steps. Energy=    -532.2918180       time=       1.68
 Minus side of path:                     625 steps. Energy=    -531.6775152       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2918180 0.62410         -531.6677214 0.97938E-02     -531.6775152  10.245  10.047   7.694  13.906
        Known (#12)                                             Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  11     -531.6775152 0.97938E-02    -531.6677214 0.62410        -532.2918180  10.245  10.047   7.694  13.906
   9     -532.2918180 0.33962        -531.9521953  1.1781        -533.1302599  11.168   9.800   1.833  58.385
  10     -533.1302599  8.6262        -524.5040647  8.5657        -533.0698040   2.806   1.666  84.469   1.267
   8     -533.0698040 0.42707        -532.6427319  1.3434        -533.9861067  16.712  16.035   3.194  33.497
   6     -533.9861067  2.0069        -531.9791570 0.29901        -532.2781679  10.903  10.235   6.324  16.919
   3     -532.2781679 0.74116E-01    -532.2040523 0.43757        -532.6416259  11.486  10.063   2.845  37.606
   1     -532.6416259  1.2175        -531.4241269  5.3028        -536.7268830  23.835  19.468   2.615  40.916
   4     -536.7268830 0.87602E-01    -536.6392811 0.36596        -537.0052404   6.181   4.966  20.838   5.135
   2     -537.0052404  4.5899        -532.4153899  3.2943        -535.7097230  15.397  12.118   5.025  21.295

 Number of TS in the path       =      9
 Number of cycles               =      8

 Elapsed time=                               163.01
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             34611 time=          69.35 %= 42.5
 OPTIM> # of energy+gradient+Hessian calls=      1076 time=          58.17 %= 35.7
