
 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 11:02:07
  [-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=    -532.8463297     RMS force=    0.9846727964E-06
 OPTIM> Final energy  =    -528.1656591     RMS force=    0.9813668703E-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=     3034.1    
 decide> The unconnected minima in the chain and their distances are:
     2       14.48     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 1.1021 Dev= 0.99% S= 19.81 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.58

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     735 steps. Energy=    -534.6561164       time=       1.90
 Minus side of path:                     604 steps. Energy=    -532.9691188       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  5.1697         -529.4863925  3.4827         -532.9691188  10.818   8.953   4.665  22.936
        *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=     2087.6    
 decide> The unconnected minima in the chain and their distances are:
     2       10.23     4     4       10.06     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2389 Dev= 0.36% S= 11.21 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.96

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     587 steps. Energy=    -530.7470032       time=       1.47
 Minus side of path:                     591 steps. Energy=    -528.1656591       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7470032  3.3258         -527.4212411 0.74442         -528.1656591   8.582   7.340   3.692  28.985
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 1.5323 Dev= 1.79% S= 15.56 time= 0.54
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=   6.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     664 steps. Energy=    -531.8440144       time=       1.67
 Minus side of path:                     661 steps. Energy=    -531.8494768       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8440144  2.7338         -529.1102367  2.7392         -531.8494768  16.512  10.164  15.437   6.931
        *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      2 steps with      1 missing connections, weight=     2052.7    
 decide> The unconnected minima in the chain and their distances are:
     5       12.71     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 105 RMS= 1.3617 Dev= 0.23% S= 17.55 time= 0.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.87

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     588 steps. Energy=    -532.9691188       time=       1.44
 Minus side of path:                     743 steps. Energy=    -534.6561164       time=       1.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9691188  3.4827         -529.4863925  5.1697         -534.6561164  10.818   8.953   4.666  22.929
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     1346.5    
 decide> The unconnected minima in the chain and their distances are:
     5        7.16     4     3        9.91     9     8        1.69     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3339 Dev= 0.57% S= 7.71 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.81
 isnewts> transition state is the same as number        1 energy=     -529.4863924992
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     742 steps. Energy=    -534.6561164       time=       2.03
 Minus side of path:                     592 steps. Energy=    -532.9691188       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  5.1697         -529.4863925  3.4827         -532.9691188  10.819   8.955   4.646  23.028
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 checkpair> Energies of the minima in the pair     3    9 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 3_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 5.8478 Dev= 1.94% S= 14.07 time= 0.29
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  21.60

 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= 0.0247 Dev= 0.03% S= 1.70 time= 0.30
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.40

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     553 steps. Energy=    -532.9691188       time=       1.54
 Minus side of path:                     545 steps. Energy=    -532.8463297       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9691188 0.12422         -532.8448981 0.14316E-02     -532.8463297   1.705   1.695  14.266   7.500
        Known (#8)                                              Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1502.1    
 decide> The unconnected minima in the chain and their distances are:
     5        8.08     3     4        9.91     8 
 

 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= 0.2738 Dev= 0.09% S= 8.52 time= 0.29
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=  10.05

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     758 steps. Energy=    -534.6561164       time=       2.10
 Minus side of path:                     511 steps. Energy=    -530.7470032       time=       1.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  3.9127         -530.7434410 0.35622E-02     -530.7470032   8.262   8.097   5.291  20.224
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to F set.

 checkpair> Energies of the minima in the pair     4    8 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 4_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.9388 Dev= 3.22% S= 14.16 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=   5.23

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     602 steps. Energy=    -536.5646447       time=       1.48
 Minus side of path:                     599 steps. Energy=    -536.1516895       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.5646447  8.5817         -527.9829017  8.1688         -536.1516895   6.783   6.560   6.475  16.526
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1819.0    
 decide> The unconnected minima in the chain and their distances are:
     5       12.21     8 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 1.3671 Dev= 1.01% S= 17.26 time= 0.56
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.05
 isnewts> transition state is the same as number        4 energy=     -529.4863924993
 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:                     580 steps. Energy=    -532.9691188       time=       1.41
 Minus side of path:                     747 steps. Energy=    -534.6561164       time=       1.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9691188  3.4827         -529.4863925  5.1697         -534.6561164  10.819   8.955   4.651  23.008
        Known (#8)                                              Known (#9)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1948.3    
 decide> The unconnected minima in the chain and their distances are:
     3        9.91     9 
 

 checkpair> Energies of the minima in the pair     3    9 are the same - checking distance ...

 tryconnect> 770-iteration DNEB run for minima 3_F and 9_S using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 770 RMS= 0.1501 Dev= 3.86% S= 21.16 time= 32.44
 Following    2 images are candidates for TS:   10   14  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         32
 DNEB run yielded 2 true transition state(s) time=   8.33

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     696 steps. Energy=    -534.7010185       time=       1.77
 Minus side of path:                     699 steps. Energy=    -534.6561164       time=       1.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7010185  5.7109         -528.9901570  5.6660         -534.6561164  25.711  10.556  13.359   8.010
        *NEW* (Placed in 12)                                    Known (#3)
 Unconnected minimum 12 found its way to F set.

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     585 steps. Energy=    -534.6561164       time=       1.45
 Minus side of path:                     568 steps. Energy=    -534.7010185       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6561164  8.3120         -526.3441422  8.3569         -534.7010185   3.560   2.939  38.499   2.779
        Known (#9)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -532.8463297 0.14316E-02    -532.8448981 0.12422        -532.9691188   1.705   1.695  14.266   7.500
   4     -532.9691188  3.4827        -529.4863925  5.1697        -534.6561164  10.818   8.953   4.666  22.929
  11     -534.6561164  8.3120        -526.3441422  8.3569        -534.7010185   3.560   2.939  38.499   2.779
  10     -534.7010185  5.7109        -528.9901570  5.6660        -534.6561164  25.711  10.556  13.359   8.010
   7     -534.6561164  3.9127        -530.7434410 0.35622E-02    -530.7470032   8.262   8.097   5.291  20.224
   2     -530.7470032  3.3258        -527.4212411 0.74442        -528.1656591   8.582   7.340   3.692  28.985

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

 Elapsed time=                               150.00
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41232 time=          82.52 %= 55.0
 OPTIM> # of energy+gradient+Hessian calls=       721 time=          39.17 %= 26.1
