
 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 11:57:34
  [-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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -534.1997122     RMS force=    0.8640551824E-06
 OPTIM> Final energy  =    -531.5047794     RMS force=    0.9923316532E-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=     16683.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.55     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 245 RMS= 0.3311 Dev= 1.07% S= 29.89 time= 3.50
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   9.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     703 steps. Energy=    -531.9013419       time=       1.80
 Minus side of path:                     934 steps. Energy=    -530.2881462       time=       2.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9013419  3.4095         -528.4918082  1.7963         -530.2881462  28.029  22.192   2.200  48.630
        *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=     7798.8    
 decide> The unconnected minima in the chain and their distances are:
     2       16.22     3     3       15.23     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.2573 Dev= 0.52% S= 17.84 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.41
 isnewts> transition state is the same as number        1 energy=     -528.4918081898
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     695 steps. Energy=    -531.9013419       time=       1.83
 Minus side of path:                     940 steps. Energy=    -530.2881462       time=       2.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9013419  3.4095         -528.4918082  1.7963         -530.2881462  28.031  22.196   2.195  48.750
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1829 Dev= 0.24% S= 16.84 time= 1.16
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.94

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     603 steps. Energy=    -534.1997122       time=       1.52
 Minus side of path:                     612 steps. Energy=    -533.2726971       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122  2.7271         -531.4726287  1.8001         -533.2726971  11.226   9.992  12.155   8.803
        Known (#1)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     9049.5    
 decide> The unconnected minima in the chain and their distances are:
     2       19.57     4     3       11.58     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 175 RMS= 0.1526 Dev= 0.25% S= 20.67 time= 1.81
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=  10.79

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     690 steps. Energy=    -531.9282653       time=       1.91
 Minus side of path:                     662 steps. Energy=    -531.6968194       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9282653 0.67646         -531.2518018 0.44502         -531.6968194  18.139  15.838   6.510  16.437
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2045 Dev= 0.26% S= 12.88 time= 0.66
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   8.65

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     678 steps. Energy=    -534.6241129       time=       2.09
 Minus side of path:                     596 steps. Energy=    -531.9013419       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129  2.7478         -531.8763090 0.25033E-01     -531.9013419   6.764   6.023   9.836  10.879
        *NEW* (Placed in 8)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     7335.4    
 decide> The unconnected minima in the chain and their distances are:
     2        4.08     7     7       16.81     3     8       13.61     5 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3746 Dev= 0.37% S= 4.18 time= 0.31
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.74

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     627 steps. Energy=    -531.6968194       time=       1.74
 Minus side of path:                     572 steps. Energy=    -531.5047794       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.6968194 0.26621         -531.4306099 0.74169E-01     -531.5047794   4.519   4.078   8.785  12.180
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_U and 7_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 175 RMS= 0.1624 Dev= 0.49% S= 18.84 time= 1.85
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   9.44

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     758 steps. Energy=    -531.9282653       time=       1.95
 Minus side of path:                     728 steps. Energy=    -530.2881462       time=       1.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9282653  2.1306         -529.7976543 0.49049         -530.2881462  29.251  26.497   5.193  20.605
        Known (#6)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 5_S and 8_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1703 Dev= 0.74% S= 15.14 time= 1.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.71

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     612 steps. Energy=    -535.2494145       time=       1.74
 Minus side of path:                     598 steps. Energy=    -533.2726971       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2494145  2.3260         -532.9234135 0.34928         -533.2726971   6.242   4.747  14.424   7.418
        *NEW* (Placed in 9)                                     Known (#5)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1329.0    
 decide> The unconnected minima in the chain and their distances are:
     3       10.99     9 
 

 tryconnect> 105-iteration DNEB run for minima 3_F and 9_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.5522 Dev= 0.98% S= 12.60 time= 0.68
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   9.05
 isnewts> transition state is the same as number        5 energy=     -531.8763089574
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     618 steps. Energy=    -531.9013419       time=       1.84
 Minus side of path:                     669 steps. Energy=    -534.6241129       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9013419 0.25033E-01     -531.8763090  2.7478         -534.6241129   6.764   6.023   9.834  10.881
        Known (#3)                                              Known (#8)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     1407.8    
 decide> The unconnected minima in the chain and their distances are:
     8       11.21     9 
 

 tryconnect> 105-iteration DNEB run for minima 8_F and 9_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3206 Dev= 0.29% S= 12.59 time= 0.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.81

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     653 steps. Energy=    -534.6241129       time=       1.74
 Minus side of path:                     622 steps. Energy=    -535.2494145       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6241129 0.74011         -533.8840039  1.3654         -535.2494145  14.144  11.231   9.057  11.814
        Known (#8)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -534.1997122  2.7271        -531.4726287  1.8001        -533.2726971  11.226   9.992  12.155   8.803
   8     -533.2726971 0.34928        -532.9234135  2.3260        -535.2494145   6.242   4.747  14.424   7.418
  10     -535.2494145  1.3654        -533.8840039 0.74011        -534.6241129  14.144  11.231   9.057  11.814
   5     -534.6241129  2.7478        -531.8763090 0.25033E-01    -531.9013419   6.764   6.023   9.836  10.879
   1     -531.9013419  3.4095        -528.4918082  1.7963        -530.2881462  28.029  22.192   2.200  48.630
   7     -530.2881462 0.49049        -529.7976543  2.1306        -531.9282653  29.251  26.497   5.193  20.605
   4     -531.9282653 0.67646        -531.2518018 0.44502        -531.6968194  18.139  15.838   6.510  16.437
   6     -531.6968194 0.26621        -531.4306099 0.74169E-01    -531.5047794   4.519   4.078   8.785  12.180

 Number of TS in the path       =      8
 Number of cycles               =      6

 Elapsed time=                               124.58
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             27293 time=          56.38 %= 45.3
 OPTIM> # of energy+gradient+Hessian calls=       659 time=          37.59 %= 30.2
