
 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 11:43:02
  [-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=    -535.3086586     RMS force=    0.8735114504E-06
 OPTIM> Final energy  =    -533.4673939     RMS force=    0.9458580542E-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=     4306.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.27     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.3649 Dev= 0.77% S= 22.17 time= 1.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.50

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     712 steps. Energy=    -536.0967470       time=       1.81
 Minus side of path:                     661 steps. Energy=    -534.9998742       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0967470  4.8752         -531.2215152  3.7784         -534.9998742  20.658  12.371   9.238  11.583
        *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=     1945.7    
 decide> The unconnected minima in the chain and their distances are:
     2       11.66     3     4        7.10     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2111 Dev= 0.31% S= 12.85 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.33

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     656 steps. Energy=    -535.3832044       time=       1.65
 Minus side of path:                     630 steps. Energy=    -533.4673939       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3832044  2.8215         -532.5617321 0.90566         -533.4673939  14.225  12.010  12.895   8.297
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3883 Dev= 0.49% S= 7.58 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.99

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     624 steps. Energy=    -535.5053530       time=       1.55
 Minus side of path:                     709 steps. Energy=    -536.0348158       time=       1.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5053530 0.52732         -534.9780294  1.0568         -536.0348158  14.640  13.519   4.337  24.669
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     758.77    
 decide> The unconnected minima in the chain and their distances are:
     5        3.51     3     4        8.15     7     7        5.58     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0945 Dev= 0.15% S= 3.57 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     636 steps. Energy=    -536.0967470       time=       1.59
 Minus side of path:                     593 steps. Energy=    -535.3832044       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0967470 0.72272         -535.3740256 0.91788E-02     -535.3832044   3.616   3.511  16.025   6.677
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2573 Dev= 0.05% S= 8.20 time= 0.39
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.31

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     611 steps. Energy=    -535.2622483       time=       1.51
 Minus side of path:                     596 steps. Energy=    -534.9998742       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2622483 0.33104         -534.9312063 0.68668E-01     -534.9998742  11.652  11.530   6.313  16.948
        *NEW* (Placed in 8)                                     Known (#4)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3951 Dev= 0.46% S= 6.11 time= 0.40
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     622 steps. Energy=    -536.0612520       time=       1.59
 Minus side of path:                     567 steps. Energy=    -535.3086586       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0612520 0.75544         -535.3058159 0.28427E-02     -535.3086586   3.538   3.461  15.645   6.839
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     634.19    
 decide> The unconnected minima in the chain and their distances are:
     4        8.59     9 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3611 Dev= 0.37% S= 8.99 time= 0.39
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   6.95

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     594 steps. Energy=    -535.8955494       time=       1.45
 Minus side of path:                     627 steps. Energy=    -535.9886668       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.8955494 0.33828         -535.5572699 0.43140         -535.9886668  13.337  12.805   3.808  28.098
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     652.98    
 decide> The unconnected minima in the chain and their distances are:
     4        8.54    10    11        3.08     9 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6001 Dev= 0.04% S= 8.66 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.26

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     582 steps. Energy=    -536.0348158       time=       1.41
 Minus side of path:                     577 steps. Energy=    -535.9886668       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0348158 0.66114E-01     -535.9687018 0.19965E-01     -535.9886668   3.628   3.426  28.496   3.755
        Known (#7)                                              Known (#11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 9_S and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.8730 Dev= 1.22% S= 3.78 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   7.69
 isnewts> transition state is the same as number        7 energy=     -535.5572699451
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     591 steps. Energy=    -535.8955494       time=       1.44
 Minus side of path:                     592 steps. Energy=    -535.9886668       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.8955494 0.33828         -535.5572699 0.43140         -535.9886668  13.338  12.806   3.792  28.217
        Known (#10)                                             Known (#11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     717.10    
 decide> The unconnected minima in the chain and their distances are:
     4        7.10     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 4_F using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 560 RMS= 0.1959 Dev= 12.16% S= 13.68 time= 18.13
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):         18
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=   5.55

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     610 steps. Energy=    -536.0612520       time=       1.49
 Minus side of path:                     606 steps. Energy=    -536.0967470       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0612520 0.26772E-01     -536.0344802 0.62267E-01     -536.0967470   3.676   3.456  28.544   3.749
        Known (#9)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     598 steps. Energy=    -536.0348158       time=       1.47
 Minus side of path:                     621 steps. Energy=    -536.0967470       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0348158  8.4496         -527.5851843  8.5116         -536.0967470   3.535   3.062  45.732   2.340
        Known (#7)                                              Known (#12)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     464.30    
 decide> The unconnected minima in the chain and their distances are:
     4        7.74    12 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7265 Dev= 0.49% S= 8.10 time= 0.39
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   7.09

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     606 steps. Energy=    -534.9998742       time=       1.48
 Minus side of path:                     664 steps. Energy=    -536.0348158       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.9998742 0.18530E-01     -534.9813441  1.0535         -536.0348158   8.301   8.155   3.956  27.047
        Known (#4)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -535.3086586 0.28427E-02    -535.3058159 0.75544        -536.0612520   3.538   3.461  15.645   6.839
  10     -536.0612520 0.26772E-01    -536.0344802 0.62267E-01    -536.0967470   3.676   3.456  28.544   3.749
  11     -536.0967470  8.5116        -527.5851843  8.4496        -536.0348158   3.535   3.062  45.732   2.340
  12     -536.0348158  1.0535        -534.9813441 0.18530E-01    -534.9998742   8.301   8.155   3.956  27.047
   1     -534.9998742  3.7784        -531.2215152  4.8752        -536.0967470  20.658  12.371   9.238  11.583
   4     -536.0967470 0.72272        -535.3740256 0.91788E-02    -535.3832044   3.616   3.511  16.025   6.677
   2     -535.3832044  2.8215        -532.5617321 0.90566        -533.4673939  14.225  12.010  12.895   8.297

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

 Elapsed time=                               123.80
 OPTIM> # of energy calls=                         78 time=           0.15 %=  0.1
 OPTIM> # of energy+gradient calls=             34503 time=          68.94 %= 55.7
 OPTIM> # of energy+gradient+Hessian calls=       551 time=          29.92 %= 24.2
