
 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 22:18:18
  [-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=    -531.9801561     RMS force=    0.8961126498E-06
 OPTIM> Final energy  =    -535.2405427     RMS force=    0.7458092430E-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      72.17438352    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     6528.1    
 decide> The unconnected minima in the chain and their distances are:
     2       18.62     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=    47
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    145 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    170 steps, energy/image=    -391.1828500     RMS=28.93804803     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   27.60     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.9614210899    
 Double-ended search iterations= 280 RMS= 0.2873 Dev= 3.60% S= 24.88 time= 4.66
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.41

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     669 steps. Energy=    -533.9067511       time=       1.72
 Minus side of path:                     668 steps. Energy=    -533.3163842       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9067511  5.1772         -528.7295543  4.5868         -533.3163842  17.810  10.232  15.640   6.841
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    11   13 from     0.11634     to     0.12558     ref=     2.8563    
 checkperc> Increasing con cutoff atoms    88  107 from     0.91406E-02 to     0.95390E-02 ref=     2.4050    
 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=     2820.5    
 decide> The unconnected minima in the chain and their distances are:
     2       11.12     3     4       11.28     1 
 

 tryconnect> Interpolation for minima 2_F and 3_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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     64 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     89 steps, energy/image=    -523.1596106     RMS=.5157422879     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   14.53     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.2981 Dev= 1.73% S= 12.15 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.04

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     650 steps. Energy=    -534.3529802       time=       1.79
 Minus side of path:                     618 steps. Energy=    -535.2405427       time=       1.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.3529802  2.2916         -532.0613938  3.1791         -535.2405427  12.263  10.198  11.514   9.293
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S 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=    61
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     47 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     72 steps, energy/image=    -516.0353490     RMS=7.021274259     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   17.40     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 175 RMS= 0.0490 Dev= 0.51% S= 11.37 time= 1.85
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   8.44

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     707 steps. Energy=    -531.9801561       time=       2.03
 Minus side of path:                     640 steps. Energy=    -533.3163842       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9801561 0.11498         -531.8651713  1.4512         -533.3163842  11.751  11.281   2.100  50.946
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     223.49    
 decide> The unconnected minima in the chain and their distances are:
     5        6.06     3 
 

 tryconnect> Interpolation for minima 3_S and 5_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=    99
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -517.4649236     RMS=10.15249544     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   13.80     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      14.77455444    
 Double-ended search iterations= 140 RMS= 0.9036 Dev= 1.49% S= 6.87 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   6.26

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     534 steps. Energy=    -533.9067511       time=       1.50
 Minus side of path:                     618 steps. Energy=    -534.8965055       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9067511 0.48615E-03     -533.9062650 0.99024         -534.8965055   5.033   5.018   5.420  19.742
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     19.929    
 decide> The unconnected minima in the chain and their distances are:
     5        2.71     6 
 

 tryconnect> Interpolation for minima 5_F and 6_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=   105
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     30 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     55 steps, energy/image=    -527.5054715     RMS=2.262694787     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      5     6 dist=   3.992     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.6615 Dev= 0.56% S= 3.31 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.26

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     587 steps. Energy=    -534.8856454       time=       1.64
 Minus side of path:                     576 steps. Energy=    -534.8965055       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.8856454 0.72520E-02     -534.8783934 0.18112E-01     -534.8965055   2.180   2.092  24.372   4.390
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5.3554    
 decide> The unconnected minima in the chain and their distances are:
     5        1.75     7 
 

 tryconnect> Interpolation for minima 5_F and 7_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=   106
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     26 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     51 steps, energy/image=    -528.8603836     RMS=.9908116869     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      5     7 dist=   2.631     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 70 RMS= 0.6161 Dev= 1.29% S= 2.29 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.49

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     623 steps. Energy=    -534.8856454       time=       1.66
 Minus side of path:                     623 steps. Energy=    -534.3529802       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.8856454  8.7101         -526.1755781  8.1774         -534.3529802   2.470   1.749  73.648   1.453
        Known (#7)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -531.9801561 0.11498        -531.8651713  1.4512        -533.3163842  11.751  11.281   2.100  50.946
   1     -533.3163842  4.5868        -528.7295543  5.1772        -533.9067511  17.810  10.232  15.640   6.841
   4     -533.9067511 0.48615E-03    -533.9062650 0.99024        -534.8965055   5.033   5.018   5.420  19.742
   5     -534.8965055 0.18112E-01    -534.8783934 0.72520E-02    -534.8856454   2.180   2.092  24.372   4.390
   6     -534.8856454  8.7101        -526.1755781  8.1774        -534.3529802   2.470   1.749  73.648   1.453
   2     -534.3529802  2.2916        -532.0613938  3.1791        -535.2405427  12.263  10.198  11.514   9.293

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                                62.91
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             16509 time=          33.58 %= 53.4
 OPTIM> # of energy+gradient+Hessian calls=       246 time=          14.59 %= 23.2
