
 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 05/25/2012 at 12:48:53
  [-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>> 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=    -448.6323444     RMS force=    0.9777542474E-06
 OPTIM> Final energy  =    -451.7197079     RMS force=    0.9823103084E-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=     6446.0    
 decide> The unconnected minima in the chain and their distances are:
     2       18.61     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1627 Dev= 0.21% S= 19.22 time= 6.73
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=  33.75

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1286 steps. Energy=    -451.7197079       time=      13.96
 Minus side of path:                    1255 steps. Energy=    -450.5543324       time=      13.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7197079  3.3664         -448.3533023  2.2010         -450.5543324   6.579   5.822  42.829   5.090
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6065.3    
 decide> The unconnected minima in the chain and their distances are:
     3       18.24     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1144 Dev= 0.27% S= 18.48 time= 6.67
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        125
 DNEB run yielded 1 true transition state(s) time=  71.73

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1620 steps. Energy=    -449.4757723       time=      22.21
 Minus side of path:                    1280 steps. Energy=    -448.6323444       time=      13.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4757723  1.3143         -448.1614398 0.47090         -448.6323444  55.626  53.092   3.875  56.256
        *NEW* (Placed in 4)                                     Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     12131.    
 decide> The unconnected minima in the chain and their distances are:
     3       18.24     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 805 RMS= 0.0166 Dev= 9.72% S= 22.86 time= 139.79
 Following    1 images are candidates for TS:    4  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        156
 DNEB run yielded 1 true transition state(s) time=  81.59
 isnewts> transition state is the same as number        2 energy=     -448.1614397874
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1627 steps. Energy=    -449.4757723       time=      18.87
 Minus side of path:                    1305 steps. Energy=    -448.6323444       time=      13.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4757723  1.3143         -448.1614398 0.47090         -448.6323444  55.624  53.089   3.882  56.160
        Known (#4)                                              Known (#1)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     12892.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.61     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1742963037    
 Double-ended search iterations= 805 RMS= 0.0192 Dev= 4.41% S= 26.02 time= 139.73
 Following    2 images are candidates for TS:    2   11  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        145
 Converged to TS (number of iterations):         21
 DNEB run yielded 2 true transition state(s) time=  97.67
 isnewts> transition state is the same as number        2 energy=     -448.1614397862
 tryconnect> Will not repeat search for TS      1 same as TS      2
 isnewts> transition state is the same as number        1 energy=     -448.3533023043
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1275 steps. Energy=    -451.7197079       time=      13.15
 Minus side of path:                    1249 steps. Energy=    -450.5543324       time=      12.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7197079  3.3664         -448.3533023  2.2010         -450.5543324   6.581   5.826  42.326   5.151
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.12406E+06
 decide> The unconnected minima in the chain and their distances are:
     3       49.87     4 
 

 tryconnect> 490-iteration DNEB run for minima 3_F and 4_S using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0221 Dev= 2.41% S= 54.43 time= 51.51
 Following    2 images are candidates for TS:    7   14  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        195
 DNEB run yielded 1 true transition state(s) time= 256.75
 isnewts> transition state is the same as number        2 energy=     -448.1614397873
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 4 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.12576E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.10     4 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 4_S using 15 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 525 RMS= 0.0855 Dev= 5.34% S= 57.32 time= 59.37
 Following    3 images are candidates for TS:    7   11   15  
 Failed to converge to TS (number of iterations):        251
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        196
 DNEB run yielded 1 true transition state(s) time= 363.87
 isnewts> transition state is the same as number        2 energy=     -448.1614397870
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 4 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.24812E+06
 decide> The unconnected minima in the chain and their distances are:
     3       49.87     4 
 

 tryconnect> 805-iteration DNEB run for minima 3_F and 4_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 805 RMS= 0.0759 Dev= 5.68% S= 58.79 time= 138.72
 Following    3 images are candidates for TS:    7   13   20  
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):        141
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        194
 DNEB run yielded 3 true transition state(s) time= 193.62
 isnewts> transition state is the same as number        2 energy=     -448.1614397875
 tryconnect> Will not repeat search for TS      3 same as TS      2

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1557 steps. Energy=    -451.4346072       time=      17.41
 Minus side of path:                    1316 steps. Energy=    -450.5543324       time=      13.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4346072  1.3550         -450.0796409 0.47469         -450.5543324  55.070  52.326   3.955  55.116
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1269 steps. Energy=    -449.3495780       time=      12.95
 Minus side of path:                    1604 steps. Energy=    -451.4346072       time=      18.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3495780 0.18233E-01     -449.3313454  2.1033         -451.4346072  49.394  48.689   2.031 107.346
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     10817.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.12     4 
 

 tryconnect> 210-iteration DNEB run for minima 4_S and 5_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0919 Dev= 0.26% S= 22.42 time= 9.49
 Following    1 images are candidates for TS:    1  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 121.00
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     21634.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.12     4 
 

 tryconnect> 805-iteration DNEB run for minima 4_S and 5_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 805 RMS= 0.0210 Dev= 4.12% S= 24.12 time= 138.30
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  21.22

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1275 steps. Energy=    -449.4757723       time=      13.07
 Minus side of path:                    1455 steps. Energy=    -451.4346072       time=      15.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4757723 0.54737         -448.9284067  2.5062         -451.4346072  22.882  22.117   1.903 114.564
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -448.6323444 0.47090        -448.1614398  1.3143        -449.4757723  55.626  53.092   3.875  56.256
   7     -449.4757723 0.54737        -448.9284067  2.5062        -451.4346072  22.882  22.117   1.903 114.564
   5     -451.4346072  1.3550        -450.0796409 0.47469        -450.5543324  55.070  52.326   3.955  55.116
   1     -450.5543324  2.2010        -448.3533023  3.3664        -451.7197079   6.579   5.822  42.829   5.090

 Number of TS in the path       =      4
 Number of cycles               =      9

 Elapsed time=                              2144.60
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            136024 time=        1011.07 %= 47.1
 OPTIM> # of energy+gradient+Hessian calls=      2255 time=         645.31 %= 30.1
