
 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 21:20:24
  [-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 = 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>> 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=    -454.2119502     RMS force=    0.9645968842E-06
 OPTIM> Final energy  =    -451.6527267     RMS force=    0.9232555382E-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=    0.16576E+07
 decide> The unconnected minima in the chain and their distances are:
     2      118.35     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3657889711E-01
 Double-ended search iterations= 805 RMS= 0.0327 Dev= 5.11% S= 143.57 time= 139.12
 Following    3 images are candidates for TS:    7   12   15  
 Converged to TS (number of iterations):        214
 Converged to TS (number of iterations):         71
 Converged to TS (number of iterations):         73
 DNEB run yielded 3 true transition state(s) time= 202.11

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1288 steps. Energy=    -449.2641409       time=      14.46
 Minus side of path:                    2435 steps. Energy=    -458.0105969       time=      38.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2641409 0.14447E-01     -449.2496936  8.7609         -458.0105969  71.796  66.066   1.546 141.010
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1287 steps. Energy=    -452.4917095       time=      14.66
 Minus side of path:                    1298 steps. Energy=    -452.7773791       time=      14.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4917095 0.47728         -452.0144344 0.76294         -452.7773791  20.831  19.726   1.575 138.416
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1330 steps. Energy=    -451.3652734       time=      15.08
 Minus side of path:                    1429 steps. Energy=    -452.4917095       time=      16.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.3652734 0.51856         -450.8467176  1.6450         -452.4917095  55.928  54.094   2.130 102.368
        *NEW* (Placed in 7)                                     Known (#5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=    0.20597E+06
 decide> The unconnected minima in the chain and their distances are:
     2       24.39     7     7       37.80     3     4       51.61     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0841 Dev= 0.03% S= 24.55 time= 13.30
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    7  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=  40.86

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1291 steps. Energy=    -451.6527267       time=      15.37
 Minus side of path:                    1301 steps. Energy=    -451.3652734       time=      15.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6527267 0.59499         -451.0577336 0.30754         -451.3652734  24.931  24.387   1.673 130.267
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 3_U and 7_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      33.86354941    
 Double-ended search iterations= 385 RMS= 0.9691 Dev= 0.22% S= 38.85 time= 32.24
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=  36.32

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1782 steps. Energy=    -451.6527267       time=      21.63
 Minus side of path:                    3636 steps. Energy=    -458.7254041       time=      67.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6527267  8.7729         -442.8797866  15.846         -458.7254041 155.537 138.648   1.695 128.601
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 525-iteration DNEB run for minima 1_S and 4_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2118582465    
 Double-ended search iterations= 525 RMS= 0.1077 Dev= 4.17% S= 63.34 time= 58.49
 Following    2 images are candidates for TS:    9   12  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time= 170.10

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1256 steps. Energy=    -454.8114834       time=      13.01
 Minus side of path:                    1232 steps. Energy=    -458.0105969       time=      12.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.8114834 0.36879         -454.4426981  3.5679         -458.0105969  23.311  18.553   2.358  92.461
        *NEW* (Placed in 9)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     41553.    
 decide> The unconnected minima in the chain and their distances are:
     8       34.64     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 8_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0288 Dev= 0.74% S= 37.42 time= 26.45
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        188
 DNEB run yielded 1 true transition state(s) time=  92.07

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1108 steps. Energy=    -457.6185991       time=      10.80
 Minus side of path:                    1178 steps. Energy=    -457.6431025       time=      11.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.6185991 0.30143         -457.3171685 0.32593         -457.6431025  14.718  14.327   5.906  36.910
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     59004.    
 decide> The unconnected minima in the chain and their distances are:
     8       17.67    11    11       37.68     1 
 

 tryconnect> 175-iteration DNEB run for minima 8_F and 11_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1437 Dev= 0.05% S= 17.82 time= 6.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  24.46

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1251 steps. Energy=    -458.7522582       time=      12.78
 Minus side of path:                    1216 steps. Energy=    -457.6431025       time=      12.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.7522582  1.6719         -457.0803656 0.56274         -457.6431025  19.789  17.654   2.134 102.161
        *NEW* (Placed in 12)                                    Known (#11)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 11_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0457 Dev= 2.09% S= 41.94 time= 32.21
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  40.14

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1233 steps. Energy=    -454.2119502       time=      13.65
 Minus side of path:                    1384 steps. Energy=    -455.5590776       time=      16.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2119502 0.35550         -453.8564500  1.7026         -455.5590776  35.526  30.337   3.404  64.042
        Known (#1)                                              *NEW* (Placed in 13)
 Unconnected minimum 13 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     5029.5    
 decide> The unconnected minima in the chain and their distances are:
     8        0.69    12    10       17.13    13 
 

 tryconnect> 70-iteration DNEB run for minima 8_F and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0631 Dev= 0.27% S= 0.69 time= 1.27
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=  14.79

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1073 steps. Energy=    -458.7522582       time=      11.36
 Minus side of path:                     979 steps. Energy=    -458.7254041       time=      10.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.7522582 0.27320E-01     -458.7249386 0.46553E-03     -458.7254041   0.689   0.687   8.057  27.056
        Known (#12)                                             Known (#8)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 10_F and 13_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0607 Dev= 0.08% S= 17.41 time= 6.94
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=  33.92

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1221 steps. Energy=    -458.1706261       time=      13.26
 Minus side of path:                    1079 steps. Energy=    -455.5590776       time=      11.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.1706261  2.6189         -455.5517340 0.73436E-02     -455.5590776  15.613  15.417   4.930  44.219
        *NEW* (Placed in 14)                                    Known (#13)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1579.7    
 decide> The unconnected minima in the chain and their distances are:
    10       11.65    14 
 

 tryconnect> 105-iteration DNEB run for minima 10_F and 14_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 107 RMS= 0.0812 Dev= 0.03% S= 11.69 time= 2.70
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=  61.09

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1169 steps. Energy=    -458.7522582       time=      11.68
 Minus side of path:                    1174 steps. Energy=    -458.1706261       time=      11.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.7522582 0.98000         -457.7722581 0.39837         -458.1706261  15.195  14.548   2.918  74.710
        Known (#12)                                             Known (#14)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -454.2119502 0.35550        -453.8564500  1.7026        -455.5590776  35.526  30.337   3.404  64.042
  11     -455.5590776 0.73436E-02    -455.5517340  2.6189        -458.1706261  15.613  15.417   4.930  44.219
  12     -458.1706261 0.39837        -457.7722581 0.98000        -458.7522582  15.195  14.548   2.918  74.710
  10     -458.7522582 0.27320E-01    -458.7249386 0.46553E-03    -458.7254041   0.689   0.687   8.057  27.056
   5     -458.7254041  15.846        -442.8797866  8.7729        -451.6527267 155.537 138.648   1.695 128.601

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                              1444.94
 OPTIM> # of energy calls=                        184 time=           1.36 %=  0.1
 OPTIM> # of energy+gradient calls=             93816 time=         696.26 %= 48.2
 OPTIM> # of energy+gradient+Hessian calls=      1252 time=         351.91 %= 24.4
