
 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 10:57:55
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.2855511     RMS force=    0.7920654060E-06
 OPTIM> Final energy  =    -537.9347047     RMS force=    0.9439804723E-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=     14733.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.51     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 245 RMS= 2.6880 Dev= 0.42% S= 30.08 time= 3.34
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   8.38

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     760 steps. Energy=    -541.8338779       time=       1.95
 Minus side of path:                     568 steps. Energy=    -537.9347047       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -541.8338779  6.9285         -534.9053878  3.0293         -537.9347047  17.295  14.118   2.550  41.959
        *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=     12278.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     4     4       22.44     1 
 

 checkpair> Energies of the minima in the pair     2    4 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 4.9035 Dev= 3.45% S= 14.53 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.77

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     599 steps. Energy=    -537.9347047       time=       1.47
 Minus side of path:                     644 steps. Energy=    -538.0863293       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.9347047  5.2544         -532.6802590  5.4061         -538.0863293  16.912  10.470  13.518   7.916
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2500 Dev= 0.44% S= 24.07 time= 2.55
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.34
 isnewts> transition state is the same as number        1 energy=     -534.9053878041
 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:                     756 steps. Energy=    -541.8338779       time=       1.94
 Minus side of path:                     567 steps. Energy=    -537.9347047       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -541.8338779  6.9285         -534.9053878  3.0293         -537.9347047  17.295  14.118   2.551  41.948
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     13336.    
 decide> The unconnected minima in the chain and their distances are:
     2        2.86     5     3       23.70     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1935 Dev= 0.27% S= 3.52 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   7.05

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     628 steps. Energy=    -538.0863293       time=       1.55
 Minus side of path:                     637 steps. Energy=    -538.5730181       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0863293  1.4847         -536.6016536  1.9714         -538.5730181  17.005  15.401   2.181  49.068
        Known (#5)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.4203 Dev= 1.46% S= 25.60 time= 3.46
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        116
 DNEB run yielded 1 true transition state(s) time=  11.04

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     719 steps. Energy=    -536.0490186       time=       1.82
 Minus side of path:                     887 steps. Energy=    -541.8338779       time=       2.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0490186  3.2903         -532.7587114  9.0752         -541.8338779  23.295  19.561   3.717  28.787
        *NEW* (Placed in 7)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     2335.9    
 decide> The unconnected minima in the chain and their distances are:
     2        2.86     5     7       13.18     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 5_U using 6 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 210 RMS= 0.0554 Dev= 2.95% S= 4.01 time= 2.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   1.88

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     569 steps. Energy=    -537.9347047       time=       1.38
 Minus side of path:                     575 steps. Energy=    -538.0863293       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.9347047  8.4481         -529.4866167  8.5997         -538.0863293   3.249   2.859  46.808   2.286
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.6161 Dev= 0.12% S= 13.52 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   5.11

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     635 steps. Energy=    -534.3593662       time=       1.57
 Minus side of path:                     578 steps. Energy=    -533.2855511       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3593662  1.4523         -532.9070977 0.37845         -533.2855511   5.827   5.477  11.331   9.443
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     2227.2    
 decide> The unconnected minima in the chain and their distances are:
     7       13.06     8 
 

 tryconnect> 105-iteration DNEB run for minima 7_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1538 Dev= 0.05% S= 13.25 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.43

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     622 steps. Energy=    -534.1642438       time=       1.53
 Minus side of path:                     672 steps. Energy=    -534.3593662       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1642438 0.55223         -533.6120163 0.74735         -534.3593662  12.938  11.827   2.828  37.841
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     526.04    
 decide> The unconnected minima in the chain and their distances are:
     7        8.07     9 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.0517 Dev= 0.10% S= 8.52 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   2.86

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     590 steps. Energy=    -534.1642438       time=       1.44
 Minus side of path:                     650 steps. Energy=    -536.0293735       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1642438 0.11361         -534.0506345  1.9787         -536.0293735   6.971   6.111   6.919  15.465
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     26.742    
 decide> The unconnected minima in the chain and their distances are:
     7        2.99    10 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0070 Dev= 0.00% S= 2.99 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   1.98

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     571 steps. Energy=    -536.0293735       time=       1.39
 Minus side of path:                     587 steps. Energy=    -536.0490186       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0293735 0.58145E-03     -536.0287920 0.20227E-01     -536.0490186   2.996   2.990   4.569  23.419
        Known (#10)                                             Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -533.2855511 0.37845        -532.9070977  1.4523        -534.3593662   5.827   5.477  11.331   9.443
   8     -534.3593662 0.74735        -533.6120163 0.55223        -534.1642438  12.938  11.827   2.828  37.841
   9     -534.1642438 0.11361        -534.0506345  1.9787        -536.0293735   6.971   6.111   6.919  15.465
  10     -536.0293735 0.58145E-03    -536.0287920 0.20227E-01    -536.0490186   2.996   2.990   4.569  23.419
   5     -536.0490186  3.2903        -532.7587114  9.0752        -541.8338779  23.295  19.561   3.717  28.787
   1     -541.8338779  6.9285        -534.9053878  3.0293        -537.9347047  17.295  14.118   2.550  41.959
   2     -537.9347047  5.2544        -532.6802590  5.4061        -538.0863293  16.912  10.470  13.518   7.916
   6     -538.0863293  8.5997        -529.4866167  8.4481        -537.9347047   3.249   2.859  46.808   2.286

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

 Elapsed time=                               102.85
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             27228 time=          54.65 %= 53.1
 OPTIM> # of energy+gradient+Hessian calls=       512 time=          27.38 %= 26.6
