
 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 11:44:01
  [-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.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.2726971     RMS force=    0.9335236956E-06
 OPTIM> Final energy  =    -532.6533047     RMS force=    0.9861961125E-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=     16060.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.23     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2695 Dev= 1.44% S= 30.15 time= 3.58
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        210
 DNEB run yielded 1 true transition state(s) time=  23.81

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     621 steps. Energy=    -534.6108661       time=       1.55
 Minus side of path:                     624 steps. Energy=    -534.6241129       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6108661 0.49576E-01     -534.5612904 0.62822E-01     -534.6241129   3.850   3.584  28.561   3.746
        *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      2 steps with      2 missing connections, weight=     7578.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.16     4     4       13.61     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1638 Dev= 1.21% S= 19.40 time= 1.88
 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 2 ...
 Plus  side of path:                     723 steps. Energy=    -534.6241129       time=       1.85
 Minus side of path:                     797 steps. Energy=    -530.6506651       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129  4.9915         -529.6325759  1.0181         -530.6506651  28.298  22.141   2.243  47.704
        Known (#4)                                              *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= 0.2012 Dev= 0.64% S= 15.17 time= 1.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     591 steps. Energy=    -533.2726971       time=       1.44
 Minus side of path:                     607 steps. Energy=    -535.2494145       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2726971 0.34928         -532.9234135  2.3260         -535.2494145   6.242   4.747  14.425   7.418
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     6676.4    
 decide> The unconnected minima in the chain and their distances are:
     2       17.40     3     4       11.21     6 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1510 Dev= 0.40% S= 19.56 time= 1.88
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=  11.75

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     633 steps. Energy=    -531.9514780       time=       1.56
 Minus side of path:                     663 steps. Energy=    -536.0967470       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9514780 0.45787         -531.4936065  4.6031         -536.0967470  19.499  18.359   2.632  40.660
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 6_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 2.1103 Dev= 0.37% S= 12.69 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.54

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     641 steps. Energy=    -534.6241129       time=       1.58
 Minus side of path:                     610 steps. Energy=    -535.2494145       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129 0.74011         -533.8840039  1.3654         -535.2494145  14.145  11.232   9.053  11.819
        Known (#4)                                              Known (#6)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2202.9    
 decide> The unconnected minima in the chain and their distances are:
     2       12.12     7     8        7.52     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5990 Dev= 0.85% S= 13.38 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.54

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     644 steps. Energy=    -532.9309229       time=       1.60
 Minus side of path:                     633 steps. Energy=    -532.6392565       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9309229  3.6276         -529.3033637  3.3359         -532.6392565   9.145   5.648  20.841   5.134
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5719 Dev= 1.05% S= 9.58 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.92

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     626 steps. Energy=    -534.6241129       time=       1.54
 Minus side of path:                     649 steps. Energy=    -535.3832044       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129 0.11980         -534.5043141 0.87889         -535.3832044   6.940   5.907  26.963   3.968
        Known (#4)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     998.02    
 decide> The unconnected minima in the chain and their distances are:
     2        3.74    10     9        9.66     7     8        3.51    11 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1811 Dev= 0.11% S= 3.91 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   2.94

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     614 steps. Energy=    -532.6392565       time=       1.51
 Minus side of path:                     628 steps. Energy=    -532.6533047       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6392565 0.64145E-01     -532.5751117 0.78193E-01     -532.6533047   4.032   3.738  28.256   3.787
        Known (#10)                                             Known (#2)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3106 Dev= 0.19% S= 9.97 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.02

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     681 steps. Energy=    -534.3412942       time=       1.70
 Minus side of path:                     633 steps. Energy=    -531.9514780       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3412942  2.5041         -531.8372022 0.11428         -531.9514780  12.154  10.383   2.781  38.478
        *NEW* (Placed in 12)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 8_U and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0953 Dev= 0.19% S= 3.57 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.37

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     585 steps. Energy=    -535.3832044       time=       1.44
 Minus side of path:                     626 steps. Energy=    -536.0967470       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3832044 0.91788E-02     -535.3740256 0.72272         -536.0967470   3.616   3.511  16.026   6.677
        Known (#11)                                             Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     223.97    
 decide> The unconnected minima in the chain and their distances are:
     9        6.07    12 
 

 tryconnect> 70-iteration DNEB run for minima 9_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5285 Dev= 0.04% S= 6.24 time= 0.40
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.64

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     573 steps. Energy=    -532.9309229       time=       1.44
 Minus side of path:                     600 steps. Energy=    -534.2643668       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9309229 0.30542E-01     -532.9003806  1.3640         -534.2643668   5.292   4.819  13.174   8.122
        Known (#9)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 13 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     50.837    
 decide> The unconnected minima in the chain and their distances are:
    13        3.70    12 
 

 tryconnect> 70-iteration DNEB run for minima 12_S and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2418 Dev= 0.09% S= 3.88 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.22

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     610 steps. Energy=    -534.3412942       time=       1.55
 Minus side of path:                     578 steps. Energy=    -534.2643668       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3412942 0.10904         -534.2322543 0.32112E-01     -534.2643668   3.984   3.705  28.832   3.711
        Known (#12)                                             Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -533.2726971 0.34928        -532.9234135  2.3260        -535.2494145   6.242   4.747  14.425   7.418
   5     -535.2494145  1.3654        -533.8840039 0.74011        -534.6241129  14.145  11.232   9.053  11.819
   7     -534.6241129 0.11980        -534.5043141 0.87889        -535.3832044   6.940   5.907  26.963   3.968
  10     -535.3832044 0.91788E-02    -535.3740256 0.72272        -536.0967470   3.616   3.511  16.026   6.677
   4     -536.0967470  4.6031        -531.4936065 0.45787        -531.9514780  19.499  18.359   2.632  40.660
   9     -531.9514780 0.11428        -531.8372022  2.5041        -534.3412942  12.154  10.383   2.781  38.478
  12     -534.3412942 0.10904        -534.2322543 0.32112E-01    -534.2643668   3.984   3.705  28.832   3.711
  11     -534.2643668  1.3640        -532.9003806 0.30542E-01    -532.9309229   5.292   4.819  13.174   8.122
   6     -532.9309229  3.6276        -529.3033637  3.3359        -532.6392565   9.145   5.648  20.841   5.134
   8     -532.6392565 0.64145E-01    -532.5751117 0.78193E-01    -532.6533047   4.032   3.738  28.256   3.787

 Number of TS in the path       =     10
 Number of cycles               =      7

 Elapsed time=                               128.71
 OPTIM> # of energy calls=                         78 time=           0.15 %=  0.1
 OPTIM> # of energy+gradient calls=             30197 time=          60.55 %= 47.0
 OPTIM> # of energy+gradient+Hessian calls=       683 time=          36.81 %= 28.6
