
 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 09:40:53
  [-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=    -534.4494624     RMS force=    0.8973323401E-06
 OPTIM> Final energy  =    -528.4997425     RMS force=    0.9296512972E-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=     6814.8    
 decide> The unconnected minima in the chain and their distances are:
     2       18.96     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 175 RMS= 0.6913 Dev= 0.96% S= 23.41 time= 1.77
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   5.18

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     773 steps. Energy=    -531.3681860       time=       2.00
 Minus side of path:                     649 steps. Energy=    -534.4494624       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.3681860  5.7307         -525.6374676  8.8120         -534.4494624  18.734  10.791   8.736  12.248
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     6680.5    
 decide> The unconnected minima in the chain and their distances are:
     2       17.87     4     4        9.91     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1661 Dev= 0.55% S= 19.88 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.88

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     670 steps. Energy=    -532.2091826       time=       1.68
 Minus side of path:                     615 steps. Energy=    -535.4392141       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2091826  5.5864         -526.6228023  8.8164         -535.4392141  14.610   9.500  10.721   9.980
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 checkpair> Energies of the minima in the pair     1    4 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 5.2074 Dev= 2.29% S= 14.33 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     602 steps. Energy=    -534.4494624       time=       1.48
 Minus side of path:                     622 steps. Energy=    -534.0047049       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4494624  8.5368         -525.9126389  8.0921         -534.0047049   4.949   4.524  23.794   4.497
        Known (#4)                                              *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      4 steps with      2 missing connections, weight=     8374.0    
 decide> The unconnected minima in the chain and their distances are:
     2       19.25     3     7       10.75     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.2487 Dev= 0.44% S= 21.97 time= 1.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=   8.22

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     710 steps. Energy=    -531.3681860       time=       1.80
 Minus side of path:                     639 steps. Energy=    -531.3841908       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.3681860  2.4498         -528.9183670  2.4658         -531.3841908  17.075  13.111  11.780   9.083
        Known (#3)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 0.9389 Dev= 1.32% S= 15.42 time= 0.58
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     691 steps. Energy=    -534.4494624       time=       1.74
 Minus side of path:                     666 steps. Energy=    -534.0047049       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4494624  3.9951         -530.4543364  3.5504         -534.0047049  21.704  10.865  12.888   8.302
        Known (#1)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     3302.6    
 decide> The unconnected minima in the chain and their distances are:
     2       14.89     8 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 8_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 2.5072 Dev= 0.28% S= 15.36 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.36

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     622 steps. Energy=    -528.4997425       time=       1.54
 Minus side of path:                     633 steps. Energy=    -530.7246939       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.4997425 0.31105         -528.1886915  2.5360         -530.7246939  11.748  11.147   3.432  31.175
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     4538.6    
 decide> The unconnected minima in the chain and their distances are:
     9       16.56     8 
 

 tryconnect> 140-iteration DNEB run for minima 8_S and 9_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4830 Dev= 0.17% S= 17.27 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.35

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     628 steps. Energy=    -531.9961663       time=       1.55
 Minus side of path:                     640 steps. Energy=    -530.7246939       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9961663  2.7865         -529.2096326  1.5151         -530.7246939  19.170  17.855   5.144  20.799
        *NEW* (Placed in 10)                                    Known (#9)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     174.63    
 decide> The unconnected minima in the chain and their distances are:
    10        5.59     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1049 Dev= 0.08% S= 5.68 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.71

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     602 steps. Energy=    -531.9961663       time=       1.48
 Minus side of path:                     608 steps. Energy=    -531.3841908       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9961663 0.94999         -531.0461759 0.33801         -531.3841908   6.322   5.590   2.810  38.072
        Known (#10)                                             Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -534.4494624  3.9951        -530.4543364  3.5504        -534.0047049  21.704  10.865  12.888   8.302
   3     -534.0047049  8.0921        -525.9126389  8.5368        -534.4494624   4.949   4.524  23.794   4.497
   1     -534.4494624  8.8120        -525.6374676  5.7307        -531.3681860  18.734  10.791   8.736  12.248
   4     -531.3681860  2.4498        -528.9183670  2.4658        -531.3841908  17.075  13.111  11.780   9.083
   8     -531.3841908 0.33801        -531.0461759 0.94999        -531.9961663   6.322   5.590   2.810  38.072
   7     -531.9961663  2.7865        -529.2096326  1.5151        -530.7246939  19.170  17.855   5.144  20.799
   6     -530.7246939  2.5360        -528.1886915 0.31105        -528.4997425  11.748  11.147   3.432  31.175

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                                75.33
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20618 time=          41.31 %= 54.8
 OPTIM> # of energy+gradient+Hessian calls=       340 time=          18.34 %= 24.3
