
 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 20:21:17
  [-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=    -451.5775602     RMS force=    0.9693886992E-06
 OPTIM> Final energy  =    -449.2022632     RMS force=    0.9506193066E-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=    0.34201E+06
 decide> The unconnected minima in the chain and their distances are:
     2       69.93     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 2_F using 20 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2224511589    
 Double-ended search iterations= 700 RMS= 0.0447 Dev= 4.83% S= 87.70 time= 104.56
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):        174
 DNEB run yielded 1 true transition state(s) time=  96.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1435 steps. Energy=    -448.8829396       time=      17.55
 Minus side of path:                    1487 steps. Energy=    -450.7087309       time=      17.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8829396 0.66582         -448.2171240  2.4916         -450.7087309  54.091  41.947   1.747 124.795
        *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      3 steps with      2 missing connections, weight=    0.12137E+06
 decide> The unconnected minima in the chain and their distances are:
     2       36.24     3     4       41.94     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 3_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0159 Dev= 0.12% S= 36.62 time= 26.19
 Following    2 images are candidates for TS:    7    9  
 Converged to TS (number of iterations):         36
 Converged to TS (number of iterations):         34
 DNEB run yielded 2 true transition state(s) time=  57.53

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1515 steps. Energy=    -449.2022632       time=      17.10
 Minus side of path:                    1314 steps. Energy=    -448.9319541       time=      13.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2022632 0.28042         -448.9218399 0.10114E-01     -448.9319541  26.186  25.888   1.600 136.248
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1346 steps. Energy=    -448.9036378       time=      14.31
 Minus side of path:                    1356 steps. Energy=    -448.9319541       time=      14.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.9036378 0.45422E-01     -448.8582155 0.73739E-01     -448.9319541  18.689  18.556   1.880 115.953
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 420-iteration DNEB run for minima 1_S and 4_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 420 RMS= 0.9120 Dev= 3.15% S= 47.76 time= 37.89
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        158
 DNEB run yielded 1 true transition state(s) time=  79.99

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1314 steps. Energy=    -450.7087309       time=      13.86
 Minus side of path:                    1344 steps. Energy=    -450.8359245       time=      14.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.7087309 0.40882E-01     -450.6678491 0.16808         -450.8359245  21.448  21.093   2.011 108.420
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     35589.    
 decide> The unconnected minima in the chain and their distances are:
     6       13.50     3     7       32.12     1 
 

 tryconnect> 140-iteration DNEB run for minima 3_U and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0122 Dev= 0.00% S= 13.53 time= 4.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  27.07

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1326 steps. Energy=    -448.8829396       time=      14.16
 Minus side of path:                    1321 steps. Energy=    -448.9036378       time=      14.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8829396 0.90678E-02     -448.8738718 0.29766E-01     -448.9036378  13.652  13.504   1.917 113.723
        Known (#3)                                              Known (#6)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 7_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0597 Dev= 1.24% S= 36.61 time= 21.38
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=  48.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1356 steps. Energy=    -450.8359245       time=      16.84
 Minus side of path:                    1325 steps. Energy=    -450.4227976       time=      16.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8359245 0.68690         -450.1490202 0.27378         -450.4227976  23.190  19.578   1.464 148.917
        Known (#7)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     10688.    
 decide> The unconnected minima in the chain and their distances are:
     8       22.03     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 8_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 210 RMS= 0.1848 Dev= 1.48% S= 25.10 time= 9.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  48.19
 isnewts> transition state is the same as number        6 energy=     -450.1490201593
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1338 steps. Energy=    -450.8359245       time=      15.96
 Minus side of path:                    1336 steps. Energy=    -450.4227976       time=      15.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8359245 0.68690         -450.1490202 0.27378         -450.4227976  23.190  19.578   1.464 148.925
        Known (#7)                                              Known (#8)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     21376.    
 decide> The unconnected minima in the chain and their distances are:
     8       22.03     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 8_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0674 Dev= 4.54% S= 33.26 time= 138.10
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  28.91

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1423 steps. Energy=    -451.5775602       time=      17.27
 Minus side of path:                    1589 steps. Energy=    -453.2016753       time=      19.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5775602  13.958         -437.6200577  15.582         -453.2016753  47.485  28.857   2.108 103.414
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     6156.4    
 decide> The unconnected minima in the chain and their distances are:
     7       18.33     9 
 

 tryconnect> 175-iteration DNEB run for minima 7_F and 9_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0660 Dev= 0.10% S= 18.56 time= 6.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  32.95

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1315 steps. Energy=    -450.8359245       time=      14.09
 Minus side of path:                    1323 steps. Energy=    -453.2016753       time=      14.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8359245 0.60655E-01     -450.7752697  2.4264         -453.2016753  18.800  18.329   6.803  32.044
        Known (#7)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -451.5775602  13.958        -437.6200577  15.582        -453.2016753  47.485  28.857   2.108 103.414
   9     -453.2016753  2.4264        -450.7752697 0.60655E-01    -450.8359245  18.800  18.329   6.803  32.044
   4     -450.8359245 0.16808        -450.6678491 0.40882E-01    -450.7087309  21.448  21.093   2.011 108.420
   1     -450.7087309  2.4916        -448.2171240 0.66582        -448.8829396  54.091  41.947   1.747 124.795
   5     -448.8829396 0.90678E-02    -448.8738718 0.29766E-01    -448.9036378  13.652  13.504   1.917 113.723
   3     -448.9036378 0.45422E-01    -448.8582155 0.73739E-01    -448.9319541  18.689  18.556   1.880 115.953
   2     -448.9319541 0.10114E-01    -448.9218399 0.28042        -449.2022632  26.186  25.888   1.600 136.248

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

 Elapsed time=                              1051.28
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             84232 time=         627.38 %= 59.7
 OPTIM> # of energy+gradient+Hessian calls=       662 time=         186.48 %= 17.7
