
 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 05/27/2012 at 22:09:48
  [-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> Constraint potential parameters read from file congeom.dat
 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -447.3016277     RMS force=    0.9644052327E-06
 OPTIM> Final energy  =    -449.6941515     RMS force=    0.9988015972E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      54.09941735    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.15562E+06
 decide> The unconnected minima in the chain and their distances are:
     2       53.73     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=     8
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    596 fraction=    0.990000 images=     5 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    621 steps, energy/image=    -12.09693673     RMS=19.42975089     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   56.12     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 560 RMS= 0.0381 Dev= 4.95% S= 63.01 time= 66.88
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 119.69
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.31124E+06
 decide> The unconnected minima in the chain and their distances are:
     2       53.73     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=     8
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    368 fraction=    0.990000 images=    21 time=       3.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    393 steps, energy/image=    -437.7718003     RMS=.3329979010     images=  22
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   148.8     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 805 RMS= 0.1336 Dev= 0.22% S= 56.66 time= 140.50
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=  39.81

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1878 steps. Energy=    -450.0091991       time=      24.69
 Minus side of path:                    1325 steps. Energy=    -447.3016277       time=      14.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.0091991  5.8741         -444.1351020  3.1665         -447.3016277  41.714  40.173   2.121 102.803
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    16   40 from     0.22529E-01 to     0.22544E-01 ref=     3.8703    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     78696.    
 decide> The unconnected minima in the chain and their distances are:
     2       42.81     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   105
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    458 fraction=    0.990000 images=     5 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    483 steps, energy/image=    -352.3688931     RMS=1.414593798     images=   6
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   46.24     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0384 Dev= 2.37% S= 53.87 time= 44.20
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        104
 DNEB run yielded 1 true transition state(s) time=  58.79

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1575 steps. Energy=    -448.0116883       time=      20.43
 Minus side of path:                    1366 steps. Energy=    -449.7525217       time=      16.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.0116883 0.39081         -447.6208779  2.1316         -449.7525217  43.768  31.682   2.372  91.922
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms   143  155 from     0.53855E-02 to     0.54621E-02 ref=     3.2975    
 checkperc> Increasing con cutoff atoms   162  169 from     0.53857E-02 to     0.61772E-02 ref=     1.9597    
 checkperc> Increasing con cutoff atoms   165  167 from     0.48653E-02 to     0.49845E-02 ref=     1.7665    
 checkperc> Increasing con cutoff atoms   184  187 from     0.14778E-02 to     0.15070E-02 ref=     2.4216    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     31880.    
 decide> The unconnected minima in the chain and their distances are:
     2        1.87     5     4       31.67     3 
 

 tryconnect> Interpolation for minima 2_F and 5_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     20 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     45 steps, energy/image=    -445.1611155     RMS=.1439484240     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   2.301     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 70 RMS= 0.2822 Dev= 4.83% S= 1.98 time= 1.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  21.93

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1297 steps. Energy=    -449.6941515       time=      13.56
 Minus side of path:                    1288 steps. Energy=    -449.7525217       time=      13.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.6941515 0.75981         -448.9343433 0.81818         -449.7525217   2.022   1.870  97.807   2.229
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 3_S and 4_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   121
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -419.7797309     RMS=10.64938909     images=   4
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   37.62     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0521 Dev= 1.16% S= 34.57 time= 31.45
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:   11  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  35.56

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1284 steps. Energy=    -448.7375584       time=      13.79
 Minus side of path:                    1408 steps. Energy=    -449.3487614       time=      14.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7375584 0.40150E-02     -448.7335435 0.61522         -449.3487614  19.164  18.576   3.814  57.159
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms   143  155 from     0.54621E-02 to     0.54785E-02 ref=     3.2975    
 checkperc> Increasing con cutoff atoms   180  186 from     0.98459E-02 to     0.98942E-02 ref=     4.1924    
 checkperc> Increasing con cutoff atoms   181  186 from     0.13631E-01 to     0.13714E-01 ref=     5.0768    
 checkperc> Increasing con cutoff atoms   182  186 from     0.10076E-01 to     0.10114E-01 ref=     2.8863    
 checkperc> Increasing con cutoff atoms   170  171 from     0.19212E-02 to     0.19545E-02 ref=     1.2326    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     3533.7    
 decide> The unconnected minima in the chain and their distances are:
     4        1.54     6     7       15.21     3 
 

 tryconnect> Interpolation for minima 4_F and 6_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     19 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     44 steps, energy/image=    -443.5231009     RMS=.2347424406E-01 images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      4     6 dist=   1.930     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 1.3729 Dev= 2.48% S= 1.70 time= 1.05
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  19.95

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1299 steps. Energy=    -448.0116883       time=      13.62
 Minus side of path:                    1294 steps. Energy=    -448.7375584       time=      13.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.0116883 0.31167         -447.7000196  1.0375         -448.7375584   1.739   1.543 131.433   1.659
        Known (#4)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> Interpolation for minima 3_S and 7_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   183
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     36 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     61 steps, energy/image=    -444.7590770     RMS=.1464826890     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   17.43     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 175 RMS= 0.0431 Dev= 0.67% S= 15.36 time= 6.52
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  22.56

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1267 steps. Energy=    -449.3487614       time=      12.89
 Minus side of path:                    1272 steps. Energy=    -450.0091991       time=      13.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3487614 0.36223E-02     -449.3451391 0.66406         -450.0091991  15.359  15.214   5.768  37.794
        Known (#7)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -447.3016277  3.1665        -444.1351020  5.8741        -450.0091991  41.714  40.173   2.121 102.803
   6     -450.0091991 0.66406        -449.3451391 0.36223E-02    -449.3487614  15.359  15.214   5.768  37.794
   4     -449.3487614 0.61522        -448.7335435 0.40150E-02    -448.7375584  19.164  18.576   3.814  57.159
   5     -448.7375584  1.0375        -447.7000196 0.31167        -448.0116883   1.739   1.543 131.433   1.659
   2     -448.0116883 0.39081        -447.6208779  2.1316        -449.7525217  43.768  31.682   2.372  91.922
   3     -449.7525217 0.81818        -448.9343433 0.75981        -449.6941515   2.022   1.870  97.807   2.229

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                               810.39
 OPTIM> # of energy calls=                         14 time=           0.10 %=  0.0
 OPTIM> # of energy+gradient calls=             66131 time=         489.63 %= 60.4
 OPTIM> # of energy+gradient+Hessian calls=       514 time=         144.46 %= 17.8
