
 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 05/28/2012 at 09:42:03
  [-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=    -526.9342646     RMS force=    0.9100655818E-06
 OPTIM> Final energy  =    -533.0074677     RMS force=    0.9839298044E-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=     32527.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.92     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 315 RMS= 0.1845 Dev= 1.03% S= 37.40 time= 5.60
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        242
 DNEB run yielded 1 true transition state(s) time=  36.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     850 steps. Energy=    -530.0281447       time=       2.23
 Minus side of path:                     770 steps. Energy=    -531.1146018       time=       1.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.0281447  1.6464         -528.3817502  2.7329         -531.1146018  26.496  23.507   2.581  41.456
        *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=     32638.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.52     4     3       26.97     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 245 RMS= 0.1526 Dev= 0.54% S= 28.36 time= 3.44
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.78

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     682 steps. Energy=    -531.1146018       time=       1.70
 Minus side of path:                     793 steps. Energy=    -533.0773862       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.1146018  2.1717         -528.9429002  4.1345         -533.0773862  27.509  24.255   4.884  21.908
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 280 RMS= 0.2478 Dev= 2.11% S= 32.39 time= 4.46
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   9.35

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     781 steps. Energy=    -527.0390260       time=       2.10
 Minus side of path:                     706 steps. Energy=    -526.8964040       time=       1.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.0390260 0.44004         -526.5989811 0.29742         -526.8964040  14.660   9.277   4.162  25.708
        *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      5 steps with      3 missing connections, weight=     15184.    
 decide> The unconnected minima in the chain and their distances are:
     2        4.93     5     3       24.43     7     7        7.85     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2513 Dev= 0.14% S= 5.57 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.95

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     675 steps. Energy=    -533.0520041       time=       1.67
 Minus side of path:                     644 steps. Energy=    -533.0074677       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0520041 0.58792E-01     -532.9932117 0.14256E-01     -533.0074677   3.970   3.611  32.067   3.337
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 3_U and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 245 RMS= 0.1665 Dev= 0.24% S= 28.35 time= 3.45
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   8.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1212 steps. Energy=    -532.4611661       time=       3.51
 Minus side of path:                     717 steps. Energy=    -527.9090897       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4611661  5.8297         -526.6314243  1.2777         -527.9090897  37.689  35.696   2.015  53.106
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1665 Dev= 0.14% S= 7.97 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=   3.85
 isnewts> transition state is the same as number        3 energy=     -526.5989810666
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     791 steps. Energy=    -527.0390260       time=       2.09
 Minus side of path:                     690 steps. Energy=    -526.8964040       time=       1.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.0390260 0.44004         -526.5989811 0.29742         -526.8964040  14.660   9.276   4.153  25.767
        Known (#6)                                              Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      4 missing connections, weight=     2265.5    
 decide> The unconnected minima in the chain and their distances are:
     8        3.58     5     4        4.79     9    10       10.45     7     7        7.85     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5881 Dev= 0.92% S= 4.27 time= 0.28
 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=  25.57

 tryconnect> 70-iteration DNEB run for minima 4_U and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1029 Dev= 0.04% S= 4.84 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   3.92

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     635 steps. Energy=    -532.4611661       time=       1.54
 Minus side of path:                     637 steps. Energy=    -531.1146018       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4611661  1.3649         -531.0962593 0.18343E-01     -531.1146018   5.409   4.787   6.053  17.677
        Known (#9)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 7_U and 10_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 1.1384 Dev= 2.26% S= 14.80 time= 0.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.19

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     754 steps. Energy=    -528.1797483       time=       1.93
 Minus side of path:                     648 steps. Energy=    -526.8964040       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.1797483  4.9518         -523.2279697  3.6684         -526.8964040  17.352  12.984   9.342  11.454
        *NEW* (Placed in 11)                                    Known (#7)
 Connection established between members of the U set.

 tryconnect> 630-iteration DNEB run for minima 1_S and 7_U using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 630 RMS= 0.0274 Dev= 4.39% S= 10.17 time= 22.81
 Following    2 images are candidates for TS:    7   14  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         20
 DNEB run yielded 2 true transition state(s) time=   5.78

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     617 steps. Energy=    -527.2011268       time=       1.51
 Minus side of path:                     617 steps. Energy=    -526.9342646       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.2011268 0.66420         -526.5369304 0.39733         -526.9342646   5.589   4.708  10.357  10.332
        *NEW* (Placed in 12)                                    Known (#1)
 Unconnected minimum 12 found its way to S set.

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     662 steps. Energy=    -526.8964040       time=       1.65
 Minus side of path:                     635 steps. Energy=    -527.2133060       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -526.8964040 0.85921E-01     -526.8104833 0.40282         -527.2133060   6.644   5.773   1.971  54.280
        Known (#7)                                              *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      3 missing connections, weight=     1084.3    
 decide> The unconnected minima in the chain and their distances are:
     8        3.58     5    10        9.97    11    13        0.83    12 
 

 tryconnect> 280-iteration DNEB run for minima 5_U and 8_F using 8 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 280 RMS= 0.0284 Dev= 2.59% S= 5.03 time= 4.49
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.65

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     652 steps. Energy=    -533.0773862       time=       1.60
 Minus side of path:                     622 steps. Energy=    -533.0520041       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.0773862  8.7588         -524.3186240  8.7334         -533.0520041   4.236   3.580  14.464   7.398
        Known (#5)                                              Known (#8)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 10_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 3.2745 Dev= 0.05% S= 10.05 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.13

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     606 steps. Energy=    -527.9090897       time=       1.48
 Minus side of path:                     708 steps. Energy=    -528.1797483       time=       1.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.9090897 0.20707         -527.7020246 0.47772         -528.1797483  10.463   9.976   2.184  48.998
        Known (#10)                                             Known (#11)
 Unconnected minimum 11 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 12_S and 13_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0038 Dev= 0.01% S= 0.83 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.23

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                     580 steps. Energy=    -527.2011268       time=       1.39
 Minus side of path:                     606 steps. Energy=    -527.2133060       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.2011268 0.10595E-02     -527.2000674 0.13239E-01     -527.2133060   0.834   0.833   4.297  24.901
        Known (#12)                                             Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -526.9342646 0.39733        -526.5369304 0.66420        -527.2011268   5.589   4.708  10.357  10.332
  13     -527.2011268 0.10595E-02    -527.2000674 0.13239E-01    -527.2133060   0.834   0.833   4.297  24.901
  10     -527.2133060 0.40282        -526.8104833 0.85921E-01    -526.8964040   6.644   5.773   1.971  54.280
   8     -526.8964040  3.6684        -523.2279697  4.9518        -528.1797483  17.352  12.984   9.342  11.454
  12     -528.1797483 0.47772        -527.7020246 0.20707        -527.9090897  10.463   9.976   2.184  48.998
   5     -527.9090897  1.2777        -526.6314243  5.8297        -532.4611661  37.689  35.696   2.015  53.106
   7     -532.4611661  1.3649        -531.0962593 0.18343E-01    -531.1146018   5.409   4.787   6.053  17.677
   2     -531.1146018  2.1717        -528.9429002  4.1345        -533.0773862  27.509  24.255   4.884  21.908
  11     -533.0773862  8.7588        -524.3186240  8.7334        -533.0520041   4.236   3.580  14.464   7.398
   4     -533.0520041 0.58792E-01    -532.9932117 0.14256E-01    -533.0074677   3.970   3.611  32.067   3.337

 Number of TS in the path       =     10
 Number of cycles               =      5

 Elapsed time=                               208.32
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             54567 time=         108.38 %= 52.0
 OPTIM> # of energy+gradient+Hessian calls=       920 time=          49.95 %= 24.0
