
 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 10:17:45
  [-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=    -533.8934689     RMS force=    0.9370030017E-06
 OPTIM> Final energy  =    -535.9666195     RMS force=    0.9878243274E-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=     9105.2    
 decide> The unconnected minima in the chain and their distances are:
     2       20.88     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 210 RMS= 0.2602 Dev= 0.43% S= 23.19 time= 2.55
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.28

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     623 steps. Energy=    -535.9666195       time=       1.57
 Minus side of path:                     602 steps. Energy=    -533.8864722       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.9666195  2.1201         -533.8464839 0.39988E-01     -533.8864722   3.735   3.570  33.604   3.184
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     8428.5    
 decide> The unconnected minima in the chain and their distances are:
     3       20.35     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1622 Dev= 0.40% S= 22.01 time= 2.54
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=  10.26

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     645 steps. Energy=    -533.9337811       time=       1.74
 Minus side of path:                     773 steps. Energy=    -533.6189959       time=       2.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9337811 0.44229         -533.4914906 0.12751         -533.6189959  12.482  10.883   2.451  43.659
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     8603.7    
 decide> The unconnected minima in the chain and their distances are:
     3        4.23     5     5       20.43     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1426 Dev= 0.10% S= 4.38 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     604 steps. Energy=    -533.6189959       time=       1.48
 Minus side of path:                     621 steps. Energy=    -533.8864722       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.6189959 0.30544E-02     -533.6159415 0.27053         -533.8864722   4.473   4.230  23.412   4.570
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0563 Dev= 0.60% S= 22.00 time= 2.53
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   8.57

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     588 steps. Energy=    -533.6151640       time=       1.43
 Minus side of path:                     623 steps. Energy=    -533.9337811       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.6151640 0.24624E-01     -533.5905396 0.34324         -533.9337811   7.065   6.786   2.287  46.781
        *NEW* (Placed in 6)                                     Known (#4)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     7411.3    
 decide> The unconnected minima in the chain and their distances are:
     6       19.50     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0722 Dev= 0.18% S= 20.28 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   7.90

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     624 steps. Energy=    -533.1047074       time=       1.54
 Minus side of path:                     644 steps. Energy=    -534.3529802       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1047074 0.17642         -532.9282899  1.4247         -534.3529802  12.780  12.102   2.181  49.060
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1970.3    
 decide> The unconnected minima in the chain and their distances are:
     6       11.51     7     8        7.63     1 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1774 Dev= 0.10% S= 12.00 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.27

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     696 steps. Energy=    -533.8712700       time=       1.76
 Minus side of path:                     633 steps. Energy=    -533.1047074       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.8712700 0.83691         -533.0343647 0.70343E-01     -533.1047074   6.966   6.380   6.278  17.043
        *NEW* (Placed in 9)                                     Known (#7)
 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= 0.0865 Dev= 0.01% S= 7.65 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=   3.06

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     647 steps. Energy=    -533.8934689       time=       1.60
 Minus side of path:                     606 steps. Energy=    -534.3626992       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.8934689 0.19769         -533.6957764 0.66692         -534.3626992   7.437   7.366   2.539  42.139
        Known (#1)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     1747.8    
 decide> The unconnected minima in the chain and their distances are:
     6       12.03     9     8        2.02    10 
 

 tryconnect> 105-iteration DNEB run for minima 6_F and 9_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2417 Dev= 0.07% S= 12.22 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.01

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     773 steps. Energy=    -533.8712700       time=       2.01
 Minus side of path:                     618 steps. Energy=    -533.6151640       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.8712700 0.33137         -533.5399030 0.75261E-01     -533.6151640  13.709  12.031   3.347  31.968
        Known (#9)                                              Known (#6)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0458 Dev= 0.14% S= 2.05 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.39

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     606 steps. Energy=    -534.3529802       time=       1.49
 Minus side of path:                     606 steps. Energy=    -534.3626992       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3529802 0.61367E-02     -534.3468435 0.15856E-01     -534.3626992   2.105   2.021  24.911   4.295
        Known (#8)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -533.8934689 0.19769        -533.6957764 0.66692        -534.3626992   7.437   7.366   2.539  42.139
   9     -534.3626992 0.15856E-01    -534.3468435 0.61367E-02    -534.3529802   2.105   2.021  24.911   4.295
   5     -534.3529802  1.4247        -532.9282899 0.17642        -533.1047074  12.780  12.102   2.181  49.060
   6     -533.1047074 0.70343E-01    -533.0343647 0.83691        -533.8712700   6.966   6.380   6.278  17.043
   8     -533.8712700 0.33137        -533.5399030 0.75261E-01    -533.6151640  13.709  12.031   3.347  31.968
   4     -533.6151640 0.24624E-01    -533.5905396 0.34324        -533.9337811   7.065   6.786   2.287  46.781
   2     -533.9337811 0.44229        -533.4914906 0.12751        -533.6189959  12.482  10.883   2.451  43.659
   3     -533.6189959 0.30544E-02    -533.6159415 0.27053        -533.8864722   4.473   4.230  23.412   4.570
   1     -533.8864722 0.39988E-01    -533.8464839  2.1201        -535.9666195   3.735   3.570  33.604   3.184

 Number of TS in the path       =      9
 Number of cycles               =      6

 Elapsed time=                                95.39
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23763 time=          47.70 %= 50.0
 OPTIM> # of energy+gradient+Hessian calls=       501 time=          27.30 %= 28.6
