
 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 20:22:04
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
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>  654 Cartesian coordinates will be optimised for  218 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=    -455.8682431     RMS force=    0.9645651013E-06
 OPTIM> Final energy  =    -455.5444822     RMS force=    0.9927468415E-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=     12995.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.51     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0875 Dev= 2.19% S= 27.25 time= 12.84
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 126.25
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     25990.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.51     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 805 RMS= 0.1272 Dev= 4.32% S= 34.89 time= 137.76
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=  62.69

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1260 steps. Energy=    -460.6408436       time=      14.48
 Minus side of path:                    1241 steps. Energy=    -458.8646876       time=      13.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.6408436  7.4849         -453.1559669  5.7087         -458.8646876  19.699  18.803   7.156  30.465
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     85417.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.64     3     3       26.36     1 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0499 Dev= 2.55% S= 43.66 time= 37.59
 Following    2 images are candidates for TS:    4    6  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         84
 DNEB run yielded 2 true transition state(s) time=  76.56

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1434 steps. Energy=    -456.5911480       time=      16.01
 Minus side of path:                    1325 steps. Energy=    -455.5444822       time=      14.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.5911480  1.6663         -454.9248061 0.61968         -455.5444822  25.591  25.028   2.477  88.022
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1246 steps. Energy=    -456.5911480       time=      14.07
 Minus side of path:                    1782 steps. Energy=    -460.6408436       time=      23.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.5911480 0.20434E-01     -456.5707140  4.0701         -460.6408436  21.739  20.432   1.609 135.515
        Known (#5)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0911 Dev= 1.73% S= 29.92 time= 12.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=  32.14

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1263 steps. Energy=    -458.0583734       time=      14.22
 Minus side of path:                    1200 steps. Energy=    -455.8682431       time=      12.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.0583734  2.4349         -455.6234590 0.24478         -455.8682431  22.799  21.426   1.835 118.801
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     831.31    
 decide> The unconnected minima in the chain and their distances are:
     5        9.40     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.6283 Dev= 1.66% S= 11.02 time= 1.06
 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= 131.16
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1533.9    
 decide> The unconnected minima in the chain and their distances are:
     3       11.53     6 
 

 tryconnect> 105-iteration DNEB run for minima 3_F and 6_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5762 Dev= 0.80% S= 13.69 time= 2.34
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 123.32
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1662.6    
 decide> The unconnected minima in the chain and their distances are:
     5        9.40     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 5_F using 21 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 735 RMS= 0.0510 Dev= 6.54% S= 29.98 time= 114.66
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  42.33
 isnewts> transition state is the same as number        1 energy=     -453.1559668944
 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:                    1235 steps. Energy=    -460.6408436       time=      12.72
 Minus side of path:                    1238 steps. Energy=    -458.8646876       time=      13.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.6408436  7.4849         -453.1559669  5.7087         -458.8646876  19.706  18.809   7.127  30.590
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     2493.9    
 decide> The unconnected minima in the chain and their distances are:
     5        9.40     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 805 RMS= 0.0794 Dev= 4.24% S= 26.75 time= 137.77
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  46.01
 isnewts> transition state is the same as number        1 energy=     -453.1559668944
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3067.8    
 decide> The unconnected minima in the chain and their distances are:
     3       11.53     6 
 

 tryconnect> 805-iteration DNEB run for minima 3_F and 6_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 805 RMS= 0.0542 Dev= 8.64% S= 33.88 time= 138.20
 Following    2 images are candidates for TS:    9   14  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         74
 DNEB run yielded 2 true transition state(s) time=  70.79
 isnewts> transition state is the same as number        1 energy=     -453.1559668914
 tryconnect> Will not repeat search for TS      1 same as TS      1

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1361 steps. Energy=    -458.8646876       time=      14.95
 Minus side of path:                    1287 steps. Energy=    -457.2259215       time=      13.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.8646876  2.9490         -455.9156857  1.3102         -457.2259215  29.280  19.941   5.340  40.821
        Known (#4)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     3902.7    
 decide> The unconnected minima in the chain and their distances are:
     7       15.74     6 
 

 tryconnect> 140-iteration DNEB run for minima 6_S and 7_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0355 Dev= 0.04% S= 15.88 time= 4.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  23.79

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1242 steps. Energy=    -457.2259215       time=      12.68
 Minus side of path:                    1227 steps. Energy=    -458.0583734       time=      12.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.2259215 0.38320         -456.8427205  1.2157         -458.0583734  16.408  15.747   6.163  35.373
        Known (#7)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -455.8682431 0.24478        -455.6234590  2.4349        -458.0583734  22.799  21.426   1.835 118.801
   7     -458.0583734  1.2157        -456.8427205 0.38320        -457.2259215  16.408  15.747   6.163  35.373
   6     -457.2259215  1.3102        -455.9156857  2.9490        -458.8646876  29.280  19.941   5.340  40.821
   1     -458.8646876  5.7087        -453.1559669  7.4849        -460.6408436  19.699  18.803   7.156  30.465
   3     -460.6408436  4.0701        -456.5707140 0.20434E-01    -456.5911480  21.739  20.432   1.609 135.515
   2     -456.5911480  1.6663        -454.9248061 0.61968        -455.5444822  25.591  25.028   2.477  88.022

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

 Elapsed time=                              1537.27
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            118173 time=         871.97 %= 56.7
 OPTIM> # of energy+gradient+Hessian calls=      1187 time=         338.80 %= 22.0
