
 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 11:50:24
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -539.2013737     RMS force=    0.9044628733E-06
 OPTIM> Final energy  =    -529.9086079     RMS force=    0.8739870662E-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=     49321.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.67     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 385 RMS= 0.1370 Dev= 5.06% S= 46.78 time= 8.65
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        150
 DNEB run yielded 1 true transition state(s) time=  14.55

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     659 steps. Energy=    -536.2842549       time=       1.67
 Minus side of path:                     553 steps. Energy=    -534.3327585       time=       1.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.2842549  2.4113         -533.8729892 0.45977         -534.3327585  12.785  12.101   1.953  54.797
        *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=     37024.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.56     4     3       23.94     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 4_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1805 Dev= 1.28% S= 32.46 time= 4.64
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        236
 DNEB run yielded 1 true transition state(s) time=  28.34

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     622 steps. Energy=    -532.6692311       time=       1.57
 Minus side of path:                     632 steps. Energy=    -532.4563274       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6692311 0.56141         -532.1078222 0.34851         -532.4563274  14.682  13.574   2.218  48.240
        *NEW* (Placed in 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      1.009492144    
 Double-ended search iterations= 245 RMS= 0.2288 Dev= 0.42% S= 28.68 time= 3.65
 Following    2 images are candidates for TS:    2    6  
 Converged to TS (number of iterations):         70
 Converged to TS (number of iterations):         36
 DNEB run yielded 2 true transition state(s) time=  11.02

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     607 steps. Energy=    -538.4806863       time=       1.52
 Minus side of path:                     746 steps. Energy=    -539.2930828       time=       1.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.4806863 0.63951E-01     -538.4167357 0.87635         -539.2930828  10.829   8.425   5.191  20.613
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     653 steps. Energy=    -538.4806863       time=       1.69
 Minus side of path:                     588 steps. Energy=    -536.6305143       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.4806863  4.4435         -534.0372236  2.5933         -536.6305143  23.587  19.397   4.992  21.434
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      4 missing connections, weight=     7469.2    
 decide> The unconnected minima in the chain and their distances are:
     2       17.60     5     6       11.50     4     3        5.25     9     8        7.05     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1704 Dev= 0.91% S= 22.59 time= 1.90
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        188
 DNEB run yielded 1 true transition state(s) time=  19.03

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     649 steps. Energy=    -532.4932861       time=       1.61
 Minus side of path:                     808 steps. Energy=    -535.2087345       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4932861  2.8606         -529.6326986  5.5760         -535.2087345  31.664  29.372   1.804  59.305
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2270 Dev= 0.08% S= 11.83 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.33

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     576 steps. Energy=    -533.0708541       time=       1.44
 Minus side of path:                     612 steps. Energy=    -534.3327585       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0708541 0.21495         -532.8559079  1.4769         -534.3327585   7.527   6.026   8.998  11.892
        *NEW* (Placed in 12)                                    Known (#4)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0354 Dev= 0.01% S= 5.26 time= 0.36
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.52

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     492 steps. Energy=    -536.2842549       time=       1.20
 Minus side of path:                     515 steps. Energy=    -536.6305143       time=       1.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.2842549 0.45176E-01     -536.2390785 0.39144         -536.6305143   5.305   5.255   1.926  55.556
        Known (#3)                                              Known (#9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1122 Dev= 0.05% S= 7.15 time= 0.41
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.20

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     591 steps. Energy=    -539.2013737       time=       1.48
 Minus side of path:                     615 steps. Energy=    -539.2930828       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -539.2013737 0.24613E-01     -539.1767604 0.11632         -539.2930828   7.516   7.052   8.775  12.194
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     3139.8    
 decide> The unconnected minima in the chain and their distances are:
     2       11.20    10    11       12.02     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 10_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2536 Dev= 0.06% S= 11.39 time= 0.76
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.28

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     600 steps. Energy=    -529.9086079       time=       1.52
 Minus side of path:                     627 steps. Energy=    -532.4932861       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.9086079 0.33971         -529.5688947  2.9244         -532.4932861  13.057  11.239   4.649  23.014
        Known (#2)                                              Known (#10)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 11_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.0472 Dev= 0.87% S= 15.90 time= 0.77
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.73

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     660 steps. Energy=    -536.2842549       time=       1.66
 Minus side of path:                     648 steps. Energy=    -536.7541114       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.2842549  3.1836         -533.1007000  3.6534         -536.7541114  20.851  11.606   9.809  10.908
        Known (#3)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     332.54    
 decide> The unconnected minima in the chain and their distances are:
    11        6.93    13 
 

 tryconnect> 70-iteration DNEB run for minima 11_F and 13_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2395 Dev= 0.08% S= 7.24 time= 0.40
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   4.71

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     524 steps. Energy=    -535.2087345       time=       1.27
 Minus side of path:                     607 steps. Energy=    -536.7541114       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2087345 0.12103E-04     -535.2087224  1.5454         -536.7541114   6.955   6.930  14.167   7.553
        Known (#11)                                             Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -539.2013737 0.24613E-01    -539.1767604 0.11632        -539.2930828   7.516   7.052   8.775  12.194
   3     -539.2930828 0.87635        -538.4167357 0.63951E-01    -538.4806863  10.829   8.425   5.191  20.613
   4     -538.4806863  4.4435        -534.0372236  2.5933        -536.6305143  23.587  19.397   4.992  21.434
   7     -536.6305143 0.39144        -536.2390785 0.45176E-01    -536.2842549   5.305   5.255   1.926  55.556
  10     -536.2842549  3.1836        -533.1007000  3.6534        -536.7541114  20.851  11.606   9.809  10.908
  11     -536.7541114  1.5454        -535.2087224 0.12103E-04    -535.2087345   6.955   6.930  14.167   7.553
   5     -535.2087345  5.5760        -529.6326986  2.8606        -532.4932861  31.664  29.372   1.804  59.305
   9     -532.4932861  2.9244        -529.5688947 0.33971        -529.9086079  13.057  11.239   4.649  23.014

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                               155.28
 OPTIM> # of energy calls=                         92 time=           0.18 %=  0.1
 OPTIM> # of energy+gradient calls=             34028 time=          68.97 %= 44.4
 OPTIM> # of energy+gradient+Hessian calls=       894 time=          48.79 %= 31.4
