
 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 05/23/2012 at 21:16:21
  [-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=    -446.7777834     RMS force=    0.8898111304E-06
 OPTIM> Final energy  =    -446.8212553     RMS force=    0.9625907686E-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=    0.19739E+06
 decide> The unconnected minima in the chain and their distances are:
     2       58.22     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.0411 Dev= 2.73% S= 69.75 time= 75.33
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        194
 DNEB run yielded 1 true transition state(s) time= 107.91

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1675 steps. Energy=    -447.0522273       time=      23.97
 Minus side of path:                    1977 steps. Energy=    -448.1414997       time=      31.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.0522273  1.0140         -446.0381801  2.1033         -448.1414997  63.569  52.115   2.693  80.936
        *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=    0.15571E+06
 decide> The unconnected minima in the chain and their distances are:
     2       51.50     4     3       26.72     1 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 4_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0616 Dev= 0.83% S= 55.14 time= 59.60
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=  46.67

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1318 steps. Energy=    -447.3016277       time=      18.23
 Minus side of path:                    1316 steps. Energy=    -446.8212553       time=      14.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3016277 0.61538         -446.6862468 0.13501         -446.8212553  14.381  13.089   8.591  25.376
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0097 Dev= 0.05% S= 26.85 time= 16.81
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=  52.05

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1760 steps. Energy=    -447.0522273       time=      29.01
 Minus side of path:                    1293 steps. Energy=    -446.7777834       time=      16.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.0522273 0.29484         -446.7573869 0.20396E-01     -446.7777834  28.798  26.741   1.705 127.858
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 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      1 missing connections, weight=    0.10170E+06
 decide> The unconnected minima in the chain and their distances are:
     5       46.68     4 
 

 tryconnect> 490-iteration DNEB run for minima 4_S and 5_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0278 Dev= 0.83% S= 49.77 time= 51.89
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        217
 DNEB run yielded 1 true transition state(s) time= 131.65

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1413 steps. Energy=    -448.2382754       time=      21.40
 Minus side of path:                    1466 steps. Energy=    -447.9185244       time=      17.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2382754  1.3450         -446.8933014  1.0252         -447.9185244  59.589  57.892   2.211  98.605
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     60875.    
 decide> The unconnected minima in the chain and their distances are:
     5       15.95     7     6       38.44     4 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0325 Dev= 0.01% S= 16.08 time= 4.20
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  46.03

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1336 steps. Energy=    -447.9185244       time=      15.84
 Minus side of path:                    1304 steps. Energy=    -447.3016277       time=      16.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.9185244 0.63292         -447.2856058 0.16022E-01     -447.3016277  16.186  15.954   4.525  48.178
        Known (#7)                                              Known (#5)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 4_S and 6_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0300 Dev= 0.32% S= 41.99 time= 32.40
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        111
 DNEB run yielded 1 true transition state(s) time=  67.56

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1506 steps. Energy=    -448.8675898       time=      17.36
 Minus side of path:                    1597 steps. Energy=    -448.1414997       time=      18.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8675898  2.2540         -446.6135821  1.5279         -448.1414997  59.554  56.027   2.527  86.273
        *NEW* (Placed in 8)                                     Known (#4)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     42755.    
 decide> The unconnected minima in the chain and their distances are:
     6       34.97     8 
 

 tryconnect> 350-iteration DNEB run for minima 6_F and 8_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0585 Dev= 0.21% S= 35.55 time= 26.39
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=  29.39

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1455 steps. Energy=    -448.8675898       time=      16.74
 Minus side of path:                    1312 steps. Energy=    -448.1636441       time=      15.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8675898 0.79508         -448.0725056 0.91138E-01     -448.1636441  31.904  29.629   2.088 104.422
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     336.65    
 decide> The unconnected minima in the chain and their distances are:
     6        6.96     9 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0130 Dev= 0.00% S= 6.96 time= 1.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        133
 DNEB run yielded 1 true transition state(s) time=  76.04
 isnewts> transition state is the same as number        7 energy=     -448.0725055685
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1405 steps. Energy=    -448.8675898       time=      17.29
 Minus side of path:                    1311 steps. Energy=    -448.1636441       time=      15.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8675898 0.79508         -448.0725056 0.91138E-01     -448.1636441  31.903  29.628   2.088 104.390
        Known (#8)                                              Known (#9)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     673.30    
 decide> The unconnected minima in the chain and their distances are:
     6        6.96     9 
 

 tryconnect> 560-iteration DNEB run for minima 6_F and 9_S using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0017 Dev= 3.95% S= 7.55 time= 68.92
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  24.17

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1287 steps. Energy=    -448.2382754       time=      15.94
 Minus side of path:                    1275 steps. Energy=    -448.1636441       time=      16.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2382754 0.11101         -448.1272696 0.36374E-01     -448.1636441   6.983   6.957   2.051 106.306
        Known (#6)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -446.7777834 0.20396E-01    -446.7573869 0.29484        -447.0522273  28.798  26.741   1.705 127.858
   1     -447.0522273  1.0140        -446.0381801  2.1033        -448.1414997  63.569  52.115   2.693  80.936
   6     -448.1414997  1.5279        -446.6135821  2.2540        -448.8675898  59.554  56.027   2.527  86.273
   7     -448.8675898 0.79508        -448.0725056 0.91138E-01    -448.1636441  31.904  29.629   2.088 104.422
   9     -448.1636441 0.36374E-01    -448.1272696 0.11101        -448.2382754   6.983   6.957   2.051 106.306
   4     -448.2382754  1.3450        -446.8933014  1.0252        -447.9185244  59.589  57.892   2.211  98.605
   5     -447.9185244 0.63292        -447.2856058 0.16022E-01    -447.3016277  16.186  15.954   4.525  48.178
   2     -447.3016277 0.61538        -446.6862468 0.13501        -446.8212553  14.381  13.089   8.591  25.376

 Number of TS in the path       =      8
 Number of cycles               =      7

 Elapsed time=                              1260.16
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             84095 time=         632.10 %= 50.2
 OPTIM> # of energy+gradient+Hessian calls=       933 time=         277.92 %= 22.1
