
 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 11:44:03
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -532.3879054     RMS force=    0.9668732620E-06
 OPTIM> Final energy  =    -536.8339524     RMS force=    0.9315893008E-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=     16868.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.65     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= 0.1944 Dev= 1.39% S= 30.53 time= 3.65
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   8.34

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     811 steps. Energy=    -536.8339524       time=       2.16
 Minus side of path:                     685 steps. Energy=    -534.6818311       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.8339524  3.5223         -533.3116802  1.3702         -534.6818311  16.929  10.698   3.941  27.151
        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=     17691.    
 decide> The unconnected minima in the chain and their distances are:
     3       26.06     1 
 

 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= 0.1877 Dev= 0.33% S= 30.65 time= 3.58
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   6.87

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     606 steps. Energy=    -534.2548200       time=       1.49
 Minus side of path:                     613 steps. Energy=    -534.3127841       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.2548200  2.3642         -531.8905907  2.4222         -534.3127841  18.836  17.847   2.583  41.423
        *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=     4483.8    
 decide> The unconnected minima in the chain and their distances are:
     3        9.67     5     4       15.30     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= 0.9108 Dev= 0.18% S= 10.00 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   2.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     560 steps. Energy=    -534.3127841       time=       1.37
 Minus side of path:                     617 steps. Energy=    -535.2319906       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3127841 0.57201         -533.7407699  1.4912         -535.2319906   9.020   8.346   6.163  17.361
        Known (#5)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4714 Dev= 0.43% S= 19.36 time= 1.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.20

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     637 steps. Energy=    -532.9044028       time=       1.58
 Minus side of path:                     714 steps. Energy=    -533.8524934       time=       1.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9044028  3.5641         -529.3402560  4.5122         -533.8524934  21.150  17.436   6.599  16.214
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     3263.8    
 decide> The unconnected minima in the chain and their distances are:
     3        5.88     6     4       11.12     7     7       11.90     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6771 Dev= 0.46% S= 6.30 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     608 steps. Energy=    -534.6818311       time=       1.51
 Minus side of path:                     601 steps. Energy=    -535.0142609       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6818311 0.13706         -534.5447687 0.46949         -535.0142609   6.110   5.692   2.763  38.731
        Known (#3)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0389 Dev= 0.05% S= 11.15 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.63

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     590 steps. Energy=    -532.9044028       time=       1.44
 Minus side of path:                     631 steps. Energy=    -534.2548200       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9044028 0.15587         -532.7485314  1.5063         -534.2548200  11.629  11.131   2.770  38.633
        Known (#7)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.8380 Dev= 0.19% S= 17.05 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   7.06

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     650 steps. Energy=    -532.3879054       time=       1.64
 Minus side of path:                     604 steps. Energy=    -533.1017664       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3879054  1.2797         -531.1081909  1.9936         -533.1017664  16.656  15.827   2.836  37.727
        Known (#1)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     127.74    
 decide> The unconnected minima in the chain and their distances are:
     9        1.74     6     8        4.97    10 
 

 tryconnect> 70-iteration DNEB run for minima 6_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.6880 Dev= 2.61% S= 2.27 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.35

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     585 steps. Energy=    -535.2319906       time=       1.52
 Minus side of path:                     597 steps. Energy=    -535.0142609       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2319906  8.4688         -526.7631588  8.2511         -535.0142609   2.474   1.736  90.959   1.176
        Known (#6)                                              Known (#9)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1458 Dev= 0.22% S= 5.05 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.08

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     620 steps. Energy=    -533.8524934       time=       1.70
 Minus side of path:                     565 steps. Energy=    -533.1017664       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.8524934 0.84274         -533.0097557 0.92011E-01     -533.1017664   5.520   4.967   7.925  13.501
        Known (#8)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -532.3879054  1.2797        -531.1081909  1.9936        -533.1017664  16.656  15.827   2.836  37.727
   9     -533.1017664 0.92011E-01    -533.0097557 0.84274        -533.8524934   5.520   4.967   7.925  13.501
   4     -533.8524934  4.5122        -529.3402560  3.5641        -532.9044028  21.150  17.436   6.599  16.214
   6     -532.9044028 0.15587        -532.7485314  1.5063        -534.2548200  11.629  11.131   2.770  38.633
   2     -534.2548200  2.3642        -531.8905907  2.4222        -534.3127841  18.836  17.847   2.583  41.423
   3     -534.3127841 0.57201        -533.7407699  1.4912        -535.2319906   9.020   8.346   6.163  17.361
   8     -535.2319906  8.4688        -526.7631588  8.2511        -535.0142609   2.474   1.736  90.959   1.176
   5     -535.0142609 0.46949        -534.5447687 0.13706        -534.6818311   6.110   5.692   2.763  38.731
   1     -534.6818311  1.3702        -533.3116802  3.5223        -536.8339524  16.929  10.698   3.941  27.151

 Number of TS in the path       =      9
 Number of cycles               =      5

 Elapsed time=                                83.05
 OPTIM> # of energy calls=                         64 time=           0.13 %=  0.2
 OPTIM> # of energy+gradient calls=             22483 time=          45.40 %= 54.7
 OPTIM> # of energy+gradient+Hessian calls=       359 time=          19.79 %= 23.8
