
 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 10:39:51
  [-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=    -531.9961663     RMS force=    0.8608141448E-06
 OPTIM> Final energy  =    -533.1879325     RMS force=    0.9561985937E-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=     4368.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.35     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 0.8083 Dev= 1.35% S= 21.80 time= 1.12
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     642 steps. Energy=    -533.1879325       time=       1.59
 Minus side of path:                     600 steps. Energy=    -532.2091826       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1879325  1.2579         -531.9300185 0.27916         -532.2091826   5.701   5.502  10.368  10.320
        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=     3592.4    
 decide> The unconnected minima in the chain and their distances are:
     3       15.32     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.5813 Dev= 1.52% S= 21.24 time= 1.12
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   6.51

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     835 steps. Energy=    -531.0120926       time=       2.19
 Minus side of path:                     616 steps. Energy=    -532.4532641       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0120926  1.7903         -529.2217993  3.2315         -532.4532641  18.702  10.843  16.290   6.568
        *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      4 steps with      2 missing connections, weight=     2817.2    
 decide> The unconnected minima in the chain and their distances are:
     3        4.35     5     4       13.98     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= 0.1338 Dev= 0.08% S= 4.43 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.07

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     574 steps. Energy=    -532.2091826       time=       1.42
 Minus side of path:                     590 steps. Energy=    -532.4532641       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2091826 0.18418E-01     -532.1907646 0.26250         -532.4532641   4.544   4.352  14.593   7.332
        Known (#3)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.4841 Dev= 0.85% S= 17.42 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     632 steps. Energy=    -532.7324610       time=       1.60
 Minus side of path:                     679 steps. Energy=    -531.8544326       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7324610  5.3606         -527.3718206  4.4826         -531.8544326  10.271   4.416  18.211   5.875
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     3052.9    
 decide> The unconnected minima in the chain and their distances are:
     4       10.73     7     7       12.20     1 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1189 Dev= 0.12% S= 10.92 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.85

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     599 steps. Energy=    -531.0120926       time=       1.50
 Minus side of path:                     592 steps. Energy=    -531.2468759       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0120926 0.28671         -530.7253829 0.52149         -531.2468759   4.741   4.262   8.991  11.900
        Known (#4)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.4521 Dev= 0.25% S= 14.17 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.99

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     666 steps. Energy=    -531.8544326       time=       1.73
 Minus side of path:                     610 steps. Energy=    -531.6048042       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8544326  2.1506         -529.7038380  1.9010         -531.6048042  13.374  11.614  17.430   6.139
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     696.11    
 decide> The unconnected minima in the chain and their distances are:
     8        8.64     7     9        3.70     1 
 

 tryconnect> 70-iteration DNEB run for minima 7_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2215 Dev= 0.10% S= 8.76 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.68

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     625 steps. Energy=    -531.8544326       time=       1.58
 Minus side of path:                     578 steps. Energy=    -531.2468759       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8544326  1.1463         -530.7081347 0.53874         -531.2468759   9.665   8.647   6.058  17.662
        Known (#7)                                              Known (#8)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.7143 Dev= 0.39% S= 4.38 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   6.01

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     609 steps. Energy=    -531.6048042       time=       1.64
 Minus side of path:                     544 steps. Energy=    -530.4431185       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.6048042  1.1636         -530.4412170 0.19015E-02     -530.4431185   9.599   9.477   6.826  15.675
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     101.15    
 decide> The unconnected minima in the chain and their distances are:
     9        3.70     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 9_F using 8 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 280 RMS= 0.2306 Dev= 1.59% S= 5.13 time= 4.64
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.31

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     623 steps. Energy=    -531.9961663       time=       1.55
 Minus side of path:                     597 steps. Energy=    -531.6048042       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9961663  8.5625         -523.4336441  8.1712         -531.6048042   4.072   3.699  30.718   3.483
        Known (#1)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -531.9961663  8.5625        -523.4336441  8.1712        -531.6048042   4.072   3.699  30.718   3.483
   6     -531.6048042  1.9010        -529.7038380  2.1506        -531.8544326  13.374  11.614  17.430   6.139
   7     -531.8544326  1.1463        -530.7081347 0.53874        -531.2468759   9.665   8.647   6.058  17.662
   5     -531.2468759 0.52149        -530.7253829 0.28671        -531.0120926   4.741   4.262   8.991  11.900
   2     -531.0120926  1.7903        -529.2217993  3.2315        -532.4532641  18.702  10.843  16.290   6.568
   3     -532.4532641 0.26250        -532.1907646 0.18418E-01    -532.2091826   4.544   4.352  14.593   7.332
   1     -532.2091826 0.27916        -531.9300185  1.2579        -533.1879325   5.701   5.502  10.368  10.320

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

 Elapsed time=                                81.25
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             22041 time=          44.50 %= 54.8
 OPTIM> # of energy+gradient+Hessian calls=       367 time=          19.99 %= 24.6
