
 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 09:53:50
  [-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>> 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=    -531.4254363     RMS force=    0.9187352584E-06
 OPTIM> Final energy  =    -533.4937306     RMS force=    0.8869974862E-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=     2351.5    
 decide> The unconnected minima in the chain and their distances are:
     2       13.30     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 7.5590 Dev= 0.32% S= 18.72 time= 0.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.54

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     659 steps. Energy=    -532.1197665       time=       1.63
 Minus side of path:                     647 steps. Energy=    -532.1227132       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665  2.7124         -529.4073688  2.7153         -532.1227132  16.684  10.169  15.423   6.938
        *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      1 steps with      1 missing connections, weight=     4703.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.30     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 805 RMS= 0.2004 Dev= 3.25% S= 22.59 time= 37.36
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.90

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     618 steps. Energy=    -532.1197665       time=       1.52
 Minus side of path:                     670 steps. Energy=    -532.7493717       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665 0.54597         -531.5737923  1.1756         -532.7493717  19.277  18.123   5.994  17.852
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     6542.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.93     6     5        1.72     4     4       14.75     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 6_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.5055 Dev= 0.71% S= 19.33 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.13

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     662 steps. Energy=    -532.1197665       time=       1.63
 Minus side of path:                     653 steps. Energy=    -532.1227132       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665  2.7009         -529.4188690  2.7038         -532.1227132  17.142  10.177  15.581   6.867
        Known (#5)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.2111 Dev= 1.82% S= 2.30 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     616 steps. Energy=    -532.1197665       time=       1.51
 Minus side of path:                     608 steps. Energy=    -532.1227132       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1197665  8.7760         -523.3437591  8.7790         -532.1227132   2.455   1.720  95.171   1.124
        Known (#5)                                              Known (#4)
 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)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0945 Dev= 0.31% S= 15.32 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=   9.39

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     601 steps. Energy=    -533.4937306       time=       1.49
 Minus side of path:                     558 steps. Energy=    -533.3770575       time=       1.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4937306 0.11826         -533.3754753 0.15822E-02     -533.3770575   2.907   2.874  15.782   6.780
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     1821.3    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     8     8        9.46     1 
 

 checkpair> Energies of the minima in the pair     2    8 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.4294 Dev= 1.04% S= 15.37 time= 0.31
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.16

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     602 steps. Energy=    -532.5989921       time=       1.46
 Minus side of path:                     657 steps. Energy=    -533.4937306       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5989921  3.6821         -528.9169055  4.5768         -533.4937306  15.523  12.618   7.441  14.379
        *NEW* (Placed in 10)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4999 Dev= 1.25% S= 10.96 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.62

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     555 steps. Energy=    -531.4254363       time=       1.32
 Minus side of path:                     678 steps. Energy=    -533.4937306       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.4254363 0.50919E-01     -531.3745174  2.1192         -533.4937306  10.403   9.488  10.301  10.387
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     869.02    
 decide> The unconnected minima in the chain and their distances are:
     2        9.54    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 10_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3309 Dev= 0.24% S= 9.93 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.69

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     558 steps. Energy=    -532.5989921       time=       1.36
 Minus side of path:                     688 steps. Energy=    -532.7976427       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5989921 0.10677         -532.4922184 0.30542         -532.7976427   8.540   7.493   2.708  39.518
        Known (#10)                                             *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     139.80    
 decide> The unconnected minima in the chain and their distances are:
     2        5.19    11 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3515 Dev= 0.71% S= 5.72 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   9.27

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     604 steps. Energy=    -533.7374985       time=       1.47
 Minus side of path:                     615 steps. Energy=    -532.6512444       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7374985  1.1903         -532.5472402 0.10400         -532.6512444  11.394  10.838   5.478  19.533
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     279.60    
 decide> The unconnected minima in the chain and their distances are:
     2        5.19    11 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 11_S using 11 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 385 RMS= 0.0183 Dev= 1.94% S= 7.05 time= 8.58
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.23

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     630 steps. Energy=    -532.7976427       time=       1.58
 Minus side of path:                     583 steps. Energy=    -533.4937306       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7976427  8.1027         -524.6949108  8.7988         -533.4937306   5.628   5.191  15.531   6.890
        Known (#11)                                             Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -531.4254363 0.50919E-01    -531.3745174  2.1192        -533.4937306  10.403   9.488  10.301  10.387
   6     -533.4937306  4.5768        -528.9169055  3.6821        -532.5989921  15.523  12.618   7.441  14.379
   8     -532.5989921 0.10677        -532.4922184 0.30542        -532.7976427   8.540   7.493   2.708  39.518
  10     -532.7976427  8.1027        -524.6949108  8.7988        -533.4937306   5.628   5.191  15.531   6.890

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

 Elapsed time=                               137.51
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             44364 time=          87.83 %= 63.9
 OPTIM> # of energy+gradient+Hessian calls=       512 time=          27.70 %= 20.1
