
 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 05/25/2012 at 12:50:57
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -449.2428646     RMS force=    0.9767780989E-06
 OPTIM> Final energy  =    -451.4137263     RMS force=    0.9936229168E-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=    0.18936E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.42     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1921616749    
 Double-ended search iterations= 595 RMS= 0.0269 Dev= 4.70% S= 64.29 time= 75.37
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        171
 DNEB run yielded 1 true transition state(s) time=  93.69

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1344 steps. Energy=    -449.4511414       time=      17.80
 Minus side of path:                    1360 steps. Energy=    -449.2428646       time=      16.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4511414 0.57950         -448.8716463 0.37122         -449.2428646  46.721  43.326   1.640 132.933
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     86456.    
 decide> The unconnected minima in the chain and their distances are:
     2       44.22     3 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 3_S using 13 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 455 RMS= 0.1093 Dev= 3.11% S= 50.68 time= 45.02
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 121.39
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.17291E+06
 decide> The unconnected minima in the chain and their distances are:
     2       44.22     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.1855 Dev= 4.22% S= 52.33 time= 137.69
 Following    2 images are candidates for TS:   12   16  
 Converged to TS (number of iterations):         54
 Converged to TS (number of iterations):         40
 DNEB run yielded 2 true transition state(s) time=  73.55

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1634 steps. Energy=    -451.4137263       time=      18.97
 Minus side of path:                    1347 steps. Energy=    -449.7929330       time=      14.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4137263  6.9470         -444.4667172  5.3262         -449.7929330  47.755  46.113   1.728 126.178
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1584 steps. Energy=    -449.4511414       time=      17.89
 Minus side of path:                    1336 steps. Energy=    -449.9537038       time=      14.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4511414  1.9976         -447.4535653  2.5001         -449.9537038  47.613  41.727   2.817  77.385
        Known (#3)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6733.3    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.3248 Dev= 1.51% S= 20.70 time= 6.67
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=  62.75

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1371 steps. Energy=    -451.6433888       time=      14.65
 Minus side of path:                    2601 steps. Energy=    -455.4122156       time=      38.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6433888 0.88168         -450.7617071  4.6505         -455.4122156  74.769  68.320   1.621 134.510
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     13467.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     5 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 805 RMS= 0.0338 Dev= 6.97% S= 33.93 time= 139.34
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  34.10
 isnewts> transition state is the same as number        2 energy=     -444.4667171708
 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:                    1349 steps. Energy=    -449.7929330       time=      17.03
 Minus side of path:                    1611 steps. Energy=    -451.4137263       time=      21.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7929330  5.3262         -444.4667172  6.9470         -451.4137263  47.755  46.113   1.727 126.212
        Known (#4)                                              Known (#2)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     38875.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.22     6     6       30.83     5 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.7372 Dev= 0.15% S= 21.30 time= 9.71
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=  28.95

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1340 steps. Energy=    -451.6433888       time=      14.37
 Minus side of path:                    1300 steps. Energy=    -451.4137263       time=      13.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6433888 0.30611         -451.3372810 0.76445E-01     -451.4137263  21.578  21.225   2.282  95.547
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 5_S and 6_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 315 RMS= 1.0270 Dev= 2.54% S= 33.94 time= 21.51
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 128.51
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     48329.    
 decide> The unconnected minima in the chain and their distances are:
     4       36.43     5 
 

 tryconnect> 350-iteration DNEB run for minima 4_F and 5_S using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 350 RMS= 0.0281 Dev= 0.54% S= 37.02 time= 26.49
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  39.74

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1378 steps. Energy=    -449.7929330       time=      14.81
 Minus side of path:                    1385 steps. Energy=    -449.9537038       time=      14.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7929330 0.38713         -449.4058017 0.54790         -449.9537038  44.094  36.781   1.719 126.851
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -449.2428646 0.37122        -448.8716463 0.57950        -449.4511414  46.721  43.326   1.640 132.933
   3     -449.4511414  1.9976        -447.4535653  2.5001        -449.9537038  47.613  41.727   2.817  77.385
   7     -449.9537038 0.54790        -449.4058017 0.38713        -449.7929330  44.094  36.781   1.719 126.851
   2     -449.7929330  5.3262        -444.4667172  6.9470        -451.4137263  47.755  46.113   1.728 126.178

 Number of TS in the path       =      4
 Number of cycles               =      7

 Elapsed time=                              1295.11
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             96873 time=         718.92 %= 55.5
 OPTIM> # of energy+gradient+Hessian calls=       993 time=         280.40 %= 21.7
