
 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 20:21:43
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
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>  654 Cartesian coordinates will be optimised for  218 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=    -454.2119502     RMS force=    0.9645968842E-06
 OPTIM> Final energy  =    -451.6527267     RMS force=    0.9232555382E-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=    0.16576E+07
 decide> The unconnected minima in the chain and their distances are:
     2      118.35     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1742963037    
 Double-ended search iterations= 805 RMS= 0.0701 Dev= 4.92% S= 136.12 time= 139.41
 Following    2 images are candidates for TS:    6   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time= 180.26

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1309 steps. Energy=    -451.7824990       time=      13.93
 Minus side of path:                    1299 steps. Energy=    -452.0690323       time=      13.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7824990 0.47697         -451.3055324 0.76350         -452.0690323  20.826  19.724   1.575 138.437
        *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=    0.54929E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.63     3     4       71.00     1 
 

 tryconnect> 595-iteration DNEB run for minima 2_F and 3_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.0784 Dev= 2.67% S= 64.09 time= 75.73
 Following    1 images are candidates for TS:    8  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 116.28

 tryconnect> 735-iteration DNEB run for minima 1_S and 4_U using 21 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 735 RMS= 0.0275 Dev= 5.33% S= 81.55 time= 114.70
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        229
 DNEB run yielded 1 true transition state(s) time= 117.23

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1328 steps. Energy=    -449.2641409       time=      13.91
 Minus side of path:                    2448 steps. Energy=    -458.0105969       time=      35.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2641409 0.14447E-01     -449.2496936  8.7609         -458.0105969  71.788  66.058   1.550 140.656
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.33221E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.96     5     6       51.61     1 
 

 tryconnect> 595-iteration DNEB run for minima 2_F and 5_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 595 RMS= 0.0448 Dev= 4.72% S= 69.80 time= 75.75
 Following    2 images are candidates for TS:    4   11  
 Converged to TS (number of iterations):         35
 Converged to TS (number of iterations):        177
 DNEB run yielded 2 true transition state(s) time= 115.55

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1289 steps. Energy=    -451.6527267       time=      13.37
 Minus side of path:                    1298 steps. Energy=    -451.3652734       time=      13.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6527267 0.59499         -451.0577336 0.30754         -451.3652734  24.931  24.387   1.673 130.267
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1323 steps. Energy=    -446.8346329       time=      13.82
 Minus side of path:                    2242 steps. Energy=    -452.1578375       time=      30.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8346329 0.34372         -446.4909132  5.6669         -452.1578375  55.675  49.679   1.938 112.471
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 525-iteration DNEB run for minima 1_S and 6_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2118582465    
 Double-ended search iterations= 525 RMS= 0.0805 Dev= 2.82% S= 62.05 time= 57.91
 Following    2 images are candidates for TS:    9   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time= 180.00

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1243 steps. Energy=    -454.8114834       time=      15.50
 Minus side of path:                    1230 steps. Energy=    -458.0105969       time=      14.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.8114834 0.36879         -454.4426981  3.5679         -458.0105969  23.312  18.553   2.354  92.613
        *NEW* (Placed in 10)                                    Known (#6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=    0.16570E+06
 decide> The unconnected minima in the chain and their distances are:
     7       37.80     5    10       48.16     1 
 

 tryconnect> 385-iteration DNEB run for minima 5_U and 7_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0534 Dev= 2.16% S= 43.80 time= 31.77
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        168
 DNEB run yielded 1 true transition state(s) time=  84.63
 isnewts> transition state is the same as number        2 energy=     -449.2496936117
 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:                    1333 steps. Energy=    -449.2641409       time=      14.13
 Minus side of path:                    3273 steps. Energy=    -458.5910073       time=      59.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2641409 0.14447E-01     -449.2496936  9.3413         -458.5910073  92.385  86.772   2.156 101.131
        Known (#5)                                              *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 1_S and 10_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0244 Dev= 1.31% S= 53.65 time= 50.79
 Following    2 images are candidates for TS:    5   10  
 Converged to TS (number of iterations):        246
 Converged to TS (number of iterations):         84
 DNEB run yielded 2 true transition state(s) time= 190.73

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1236 steps. Energy=    -452.8965336       time=      12.58
 Minus side of path:                    2116 steps. Energy=    -458.5910073       time=      27.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8965336 0.31741         -452.5791226  6.0119         -458.5910073  77.068  73.054   2.025 107.671
        *NEW* (Placed in 12)                                    Known (#11)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1265 steps. Energy=    -456.2671933       time=      12.95
 Minus side of path:                    1382 steps. Energy=    -458.5910073       time=      14.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.2671933 0.38756         -455.8796328  2.7114         -458.5910073  30.545  29.301   1.922 113.403
        *NEW* (Placed in 13)                                    Known (#11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.15956E+06
 decide> The unconnected minima in the chain and their distances are:
     7       37.80     5    11       37.21     1 
 

 tryconnect> 805-iteration DNEB run for minima 5_U and 7_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 805 RMS= 0.1118 Dev= 7.54% S= 42.47 time= 138.44
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=  32.68

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1805 steps. Energy=    -451.6527267       time=      21.97
 Minus side of path:                    3873 steps. Energy=    -458.5910073       time=      75.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6527267  8.7729         -442.8797866  15.711         -458.5910073 142.835 118.200   1.648 132.308
        Known (#2)                                              Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 11_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0436 Dev= 0.79% S= 38.74 time= 31.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  33.71

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1638 steps. Energy=    -458.5910073       time=      19.73
 Minus side of path:                    1250 steps. Energy=    -454.2119502       time=      12.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.5910073  4.6747         -453.9162795 0.29567         -454.2119502  39.257  37.228   2.235  97.527
        Known (#11)                                             Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -454.2119502 0.29567        -453.9162795  4.6747        -458.5910073  39.257  37.228   2.235  97.527
   9     -458.5910073  15.711        -442.8797866  8.7729        -451.6527267 142.835 118.200   1.648 132.308

 Number of TS in the path       =      2
 Number of cycles               =      5

 Elapsed time=                              2217.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            152830 time=        1132.05 %= 51.0
 OPTIM> # of energy+gradient+Hessian calls=      1931 time=         531.78 %= 24.0
