
 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 21:30:53
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -445.2490701     RMS force=    0.9988529171E-06
 OPTIM> Final energy  =    -446.4469057     RMS force=    0.9815358662E-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=    0.30755E+06
 decide> The unconnected minima in the chain and their distances are:
     2       67.50     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 2_F using 20 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1238691290    
 Double-ended search iterations= 700 RMS= 0.1067 Dev= 8.25% S= 89.54 time= 106.83
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):        149
 DNEB run yielded 1 true transition state(s) time= 132.04

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1323 steps. Energy=    -449.8496282       time=      18.01
 Minus side of path:                    1496 steps. Energy=    -450.7335018       time=      20.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.8496282  4.3812         -445.4683792  5.2651         -450.7335018  46.739  33.082   3.494  62.398
        *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=    0.52420E+06
 decide> The unconnected minima in the chain and their distances are:
     2       65.89     3     4       61.99     1 
 

 tryconnect> 665-iteration DNEB run for minima 2_F and 3_U using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1519928728E-01
 Double-ended search iterations= 665 RMS= 0.0509 Dev= 1.32% S= 75.91 time= 96.06
 Following    2 images are candidates for TS:    4   10  
 Converged to TS (number of iterations):         36
 Converged to TS (number of iterations):        118
 DNEB run yielded 2 true transition state(s) time= 102.30

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1302 steps. Energy=    -446.4469057       time=      16.47
 Minus side of path:                    1383 steps. Energy=    -446.5481851       time=      15.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.4469057 0.29037         -446.1565392 0.39165         -446.5481851  36.029  35.331   1.894 115.105
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1397 steps. Energy=    -448.8682363       time=      16.56
 Minus side of path:                    1399 steps. Energy=    -446.5481851       time=      19.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8682363  2.4902         -446.3780588 0.17013         -446.5481851  52.467  50.627   2.349  92.814
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 630-iteration DNEB run for minima 1_S and 4_U using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1238691290    
 Double-ended search iterations= 630 RMS= 0.0270 Dev= 5.73% S= 88.83 time= 86.78
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        205
 DNEB run yielded 1 true transition state(s) time= 112.18

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1776 steps. Energy=    -448.5066060       time=      24.33
 Minus side of path:                    1686 steps. Energy=    -447.4142980       time=      25.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.5066060  2.9441         -445.5625484  1.8517         -447.4142980  94.833  80.707   1.693 128.753
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.12672E+06
 decide> The unconnected minima in the chain and their distances are:
     6       41.42     8     8       38.18     1 
 

 tryconnect> 420-iteration DNEB run for minima 6_F and 8_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1448 Dev= 3.10% S= 49.34 time= 38.75
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=  49.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1643 steps. Energy=    -448.3511272       time=      19.56
 Minus side of path:                    1469 steps. Energy=    -448.8682363       time=      16.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3511272  3.7944         -444.5566976  4.3115         -448.8682363  61.952  49.801   3.183  68.480
        *NEW* (Placed in 9)                                     Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 8_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0373 Dev= 1.56% S= 40.46 time= 32.28
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 130.80
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     52939.    
 decide> The unconnected minima in the chain and their distances are:
     9       37.55     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 9_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0818 Dev= 2.31% S= 44.32 time= 32.37
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  39.26

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1311 steps. Energy=    -445.2490701       time=      15.78
 Minus side of path:                    1667 steps. Energy=    -453.8621904       time=      23.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2490701  5.0596         -440.1895034  13.673         -453.8621904  49.864  44.235   3.300  66.069
        Known (#1)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.10588E+06
 decide> The unconnected minima in the chain and their distances are:
     9       37.55     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 9_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0462 Dev= 5.54% S= 48.62 time= 142.10
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=  38.51

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1348 steps. Energy=    -447.4142980       time=      16.43
 Minus side of path:                    1460 steps. Energy=    -448.3511272       time=      19.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4142980  3.8019         -443.6124212  4.7387         -448.3511272  47.780  26.485   2.956  73.741
        Known (#8)                                              Known (#9)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=    0.11128E+06
 decide> The unconnected minima in the chain and their distances are:
     8       38.18     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 8_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2245626974E-01
 Double-ended search iterations= 805 RMS= 0.0249 Dev= 4.30% S= 45.41 time= 142.43
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  33.40

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1387 steps. Energy=    -447.4369453       time=      17.81
 Minus side of path:                    1330 steps. Energy=    -445.2490701       time=      16.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4369453  2.8600         -444.5769912 0.67208         -445.2490701  46.869  45.310   1.720 126.760
        *NEW* (Placed in 11)                                    Known (#1)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3363.2    
 decide> The unconnected minima in the chain and their distances are:
     8       14.98    11 
 

 tryconnect> 140-iteration DNEB run for minima 8_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0236 Dev= 0.02% S= 15.02 time= 4.61
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=  36.23

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1254 steps. Energy=    -447.4369453       time=      13.34
 Minus side of path:                    1312 steps. Energy=    -447.4142980       time=      14.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4369453 0.14681         -447.2901370 0.12416         -447.4142980  15.205  14.983   1.900 114.733
        Known (#11)                                             Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -445.2490701 0.67208        -444.5769912  2.8600        -447.4369453  46.869  45.310   1.720 126.760
   9     -447.4369453 0.14681        -447.2901370 0.12416        -447.4142980  15.205  14.983   1.900 114.733
   7     -447.4142980  3.8019        -443.6124212  4.7387        -448.3511272  47.780  26.485   2.956  73.741
   5     -448.3511272  3.7944        -444.5566976  4.3115        -448.8682363  61.952  49.801   3.183  68.480
   3     -448.8682363  2.4902        -446.3780588 0.17013        -446.5481851  52.467  50.627   2.349  92.814
   2     -446.5481851 0.39165        -446.1565392 0.29037        -446.4469057  36.029  35.331   1.894 115.105

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                              1687.09
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            131763 time=         995.21 %= 59.0
 OPTIM> # of energy+gradient+Hessian calls=      1021 time=         303.36 %= 18.0
