
 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 05/27/2012 at 22:11:45
  [-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> Constraint potential parameters read from file congeom.dat
 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -533.9376822     RMS force=    0.8170521373E-06
 OPTIM> Final energy  =    -534.7747649     RMS force=    0.8124047901E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      21.72616475    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     9831.2    
 decide> The unconnected minima in the chain and their distances are:
     2       21.40     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    26
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     82 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    107 steps, energy/image=    -466.6432446     RMS=15.50115737     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   26.28     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0685 Dev= 2.27% S= 23.24 time= 3.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   8.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     676 steps. Energy=    -535.8806147       time=       1.66
 Minus side of path:                     601 steps. Energy=    -534.3329530       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.8806147  2.0418         -533.8388629 0.49409         -534.3329530  20.354  19.009   3.032  35.292
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    18   20 from     0.24507E-01 to     0.25198E-01 ref=     2.4248    
 checkperc> Increasing con cutoff atoms    31   35 from     0.59321E-02 to     0.59941E-02 ref=     2.0311    
 checkperc> Increasing con cutoff atoms    18   20 from     0.25198E-01 to     0.25470E-01 ref=     2.4248    
 checkperc> Increasing con cutoff atoms    19   20 from     0.32303E-02 to     0.34769E-02 ref=     1.0115    
 checkperc> Increasing con cutoff atoms    55   56 from     0.28568E-02 to     0.30193E-02 ref=     1.0126    
 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=     3995.8    
 decide> The unconnected minima in the chain and their distances are:
     2        9.08     4     3       14.79     1 
 

 tryconnect> Interpolation for minima 2_F and 4_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    85
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     23 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     48 steps, energy/image=    -522.8114304     RMS=7.744491770     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   15.18     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 3.6988 Dev= 0.53% S= 9.17 time= 1.14
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         34
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=   7.59
 isnewts> transition state is the same as number        2 energy=     -534.2502576319
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     599 steps. Energy=    -534.3329530       time=       1.44
 Minus side of path:                     598 steps. Energy=    -534.7747649       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3329530 0.82695E-01     -534.2502576 0.52451         -534.7747649   9.299   9.082   2.920  36.647
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     614 steps. Energy=    -534.3329530       time=       1.48
 Minus side of path:                     614 steps. Energy=    -534.7747649       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3329530 0.82695E-01     -534.2502576 0.52451         -534.7747649   9.299   9.082   2.918  36.669
        Known (#4)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> Interpolation for minima 1_S and 3_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    55
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     57 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     82 steps, energy/image=    -499.7559108     RMS=13.18359790     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   20.31     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 210 RMS= 0.0605 Dev= 0.47% S= 15.50 time= 2.56
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   7.19

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     711 steps. Energy=    -537.4737724       time=       1.77
 Minus side of path:                     667 steps. Energy=    -533.9376822       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.4737724  3.8423         -533.6314813 0.30620         -533.9376822  19.622  18.148   3.401  31.465
        *NEW* (Placed in 5)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    12   24 from     0.19306E-01 to     0.20334E-01 ref=     2.4623    
 checkperc> Increasing con cutoff atoms    12   25 from     0.47518E-01 to     0.48257E-01 ref=     2.5607    
 checkperc> Increasing con cutoff atoms    13   23 from     0.38212E-01 to     0.38403E-01 ref=     3.2408    
 checkperc> Increasing con cutoff atoms    13   25 from     0.12202     to     0.12473     ref=     2.2198    
 checkperc> Increasing con cutoff atoms    13   36 from     0.14839     to     0.18654     ref=     4.9106    
 checkperc> Increasing con cutoff atoms    14   19 from     0.10203E-01 to     0.10206E-01 ref=     2.4438    
 checkperc> Increasing con cutoff atoms    17   18 from     0.19324E-02 to     0.20108E-02 ref=     1.2257    
 checkperc> Increasing con cutoff atoms    23   24 from     0.13063E-01 to     0.14575E-01 ref=     2.2467    
 checkperc> Increasing con cutoff atoms    24   38 from     0.67922E-01 to     0.68961E-01 ref=     2.8435    
 checkperc> Increasing con cutoff atoms    31   35 from     0.59941E-02 to     0.66950E-02 ref=     2.0311    
 checkperc> Increasing con cutoff atoms    57   59 from     0.51818E-02 to     0.52608E-02 ref=     1.5418    
 checkperc> Increasing con cutoff atoms    59   64 from     0.11860E-01 to     0.12165E-01 ref=     2.1628    
 checkperc> Increasing con cutoff atoms    61   62 from     0.14512E-01 to     0.18780E-01 ref=     2.1515    
 checkperc> Increasing con cutoff atoms    65   67 from     0.12298E-02 to     0.12890E-02 ref=     1.3185    
 checkperc> Increasing con cutoff atoms    76   78 from     0.12793E-02 to     0.22575E-02 ref=     1.0901    
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1235.5    
 decide> The unconnected minima in the chain and their distances are:
     3       10.72     5 
 

 tryconnect> Interpolation for minima 3_F and 5_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    78
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     32 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     57 steps, energy/image=    -515.7228773     RMS=14.17125005     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   17.02     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 175 RMS= 0.0744 Dev= 0.51% S= 10.90 time= 1.79
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.22

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     598 steps. Energy=    -535.8806147       time=       1.44
 Minus side of path:                     673 steps. Energy=    -537.4737724       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.8806147 0.30972         -535.5708923  1.9029         -537.4737724  12.560  10.721   2.759  38.776
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -533.9376822 0.30620        -533.6314813  3.8423        -537.4737724  19.622  18.148   3.401  31.465
   5     -537.4737724  1.9029        -535.5708923 0.30972        -535.8806147  12.560  10.721   2.759  38.776
   1     -535.8806147  2.0418        -533.8388629 0.49409        -534.3329530  20.354  19.009   3.032  35.292
   2     -534.3329530 0.82695E-01    -534.2502576 0.52451        -534.7747649   9.299   9.082   2.920  36.647

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                54.61
 OPTIM> # of energy calls=                          8 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             14510 time=          28.78 %= 52.7
 OPTIM> # of energy+gradient+Hessian calls=       277 time=          14.84 %= 27.2
