
 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 22:16:57
  [-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 = 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=    -533.5989010     RMS force=    0.9218093822E-06
 OPTIM> Final energy  =    -530.5852566     RMS force=    0.9815690227E-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      81.34456120    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3625.0    
 decide> The unconnected minima in the chain and their distances are:
     2       15.28     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=    67
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    292 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    317 steps, energy/image=    -509.8860560     RMS=.9958418215     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   34.60     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 350 RMS= 1.1501 Dev= 4.23% S= 23.21 time= 7.40
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.58

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     666 steps. Energy=    -533.4986140       time=       1.91
 Minus side of path:                     649 steps. Energy=    -533.1273492       time=       1.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4986140  5.2194         -528.2792499  4.8481         -533.1273492  19.461  10.743  12.585   8.502
        *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      3 steps with      2 missing connections, weight=     2680.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.77     4     3        3.94     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=    61
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    105 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    130 steps, energy/image=    -500.6377938     RMS=2.459149088     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   17.03     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.4184 Dev= 0.83% S= 15.86 time= 1.86
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.79

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     625 steps. Energy=    -533.4986140       time=       1.69
 Minus side of path:                     564 steps. Energy=    -531.0960020       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4986140  2.6040         -530.8946149 0.20139         -531.0960020   9.224   8.553   2.949  36.286
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    24   28 from     0.31624E-01 to     0.31807E-01 ref=     2.4467    
 checkperc> Increasing con cutoff atoms    26   30 from     0.10999E-01 to     0.11580E-01 ref=     2.1542    
 checkperc> Increasing con cutoff atoms    26   37 from     0.11523E-01 to     0.12113E-01 ref=     2.4103    
 checkperc> Increasing con cutoff atoms    36   37 from     0.31653E-02 to     0.33049E-02 ref=     1.2313    
 checkperc> Increasing con cutoff atoms    40   41 from     0.15656E-02 to     0.16796E-02 ref=     1.0922    
 checkperc> Increasing con cutoff atoms    40   43 from     0.14827E-01 to     0.15299E-01 ref=     2.1664    
 checkperc> Increasing con cutoff atoms    57   74 from     0.33785E-01 to     0.34297E-01 ref=     3.8641    
 checkperc> Increasing con cutoff atoms    74   76 from     0.65539E-02 to     0.68648E-02 ref=     1.5434    
 checkperc> Increasing con cutoff atoms    87   88 from     0.15070E-01 to     0.16444E-01 ref=     2.1262    
 checkperc> Increasing con cutoff atoms    94  101 from     0.42589E-02 to     0.43885E-02 ref=     2.8182    
 checkperc> Increasing con cutoff atoms    94  102 from     0.55447E-02 to     0.55643E-02 ref=     3.8980    
 checkperc> Increasing con cutoff atoms    95  101 from     0.44339E-02 to     0.46285E-02 ref=     3.9008    
 checkperc> Increasing con cutoff atoms    95  102 from     0.56277E-02 to     0.57093E-02 ref=     4.9807    
 checkperc> Increasing con cutoff atoms    95  103 from     0.25494E-02 to     0.25526E-02 ref=     3.4197    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S 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=   104
 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=    -527.4666791     RMS=1.960641120     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   12.61     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 0.0954 Dev= 0.23% S= 3.97 time= 0.67
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.55

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     569 steps. Energy=    -533.4986140       time=       1.58
 Minus side of path:                     577 steps. Energy=    -533.5989010       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4986140 0.14484         -533.3537749 0.24513         -533.5989010   4.086   3.942  10.446  10.243
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1856.5    
 decide> The unconnected minima in the chain and their distances are:
     2       12.11     5     5        4.25     4 
 

 tryconnect> Interpolation for minima 2_F and 5_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=    66
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     77 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    102 steps, energy/image=    -521.2568217     RMS=1.697471327     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   13.83     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1751 Dev= 1.92% S= 13.52 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.71

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     622 steps. Energy=    -531.0960020       time=       1.75
 Minus side of path:                     622 steps. Energy=    -530.5852566       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0960020  1.7780         -529.3179722  1.2673         -530.5852566  14.393  13.587   2.090  51.189
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> Interpolation for minima 4_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=   104
 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=    -519.7388800     RMS=.9291350475     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   13.11     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      17.10339358    
 Double-ended search iterations= 105 RMS= 1.2054 Dev= 1.40% S= 4.87 time= 0.67
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=   8.86

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     572 steps. Energy=    -532.5018227       time=       1.37
 Minus side of path:                     691 steps. Energy=    -533.1273492       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5018227 0.72016         -531.7816641  1.3457         -533.1273492  13.008  11.892   6.107  17.522
        *NEW* (Placed in 7)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    42   43 from     0.10730E-02 to     0.12642E-02 ref=     1.0906    
 checkperc> Increasing con cutoff atoms    57   74 from     0.34297E-01 to     0.34496E-01 ref=     3.8641    
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     154.15    
 decide> The unconnected minima in the chain and their distances are:
     5        4.25     4 
 

 tryconnect> Interpolation for minima 4_S and 5_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   104
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     27 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     52 steps, energy/image=    -527.5161371     RMS=.5554168091     images=  15
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   5.591     Attempts, images and iterations=     1    12   420
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 420 RMS= 0.1532 Dev= 4.55% S= 5.73 time= 10.29
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.13

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     597 steps. Energy=    -533.4986140       time=       1.61
 Minus side of path:                     569 steps. Energy=    -533.1273492       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4986140  8.6684         -524.8302396  8.2971         -533.1273492   4.581   4.252  23.815   4.493
        Known (#5)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -533.5989010 0.24513        -533.3537749 0.14484        -533.4986140   4.086   3.942  10.446  10.243
   1     -533.4986140  5.2194        -528.2792499  4.8481        -533.1273492  19.461  10.743  12.585   8.502
   6     -533.1273492  8.2971        -524.8302396  8.6684        -533.4986140   4.581   4.252  23.815   4.493
   2     -533.4986140  2.6040        -530.8946149 0.20139        -531.0960020   9.224   8.553   2.949  36.286
   4     -531.0960020  1.7780        -529.3179722  1.2673        -530.5852566  14.393  13.587   2.090  51.189

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                                78.58
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             23094 time=          46.86 %= 59.6
 OPTIM> # of energy+gradient+Hessian calls=       283 time=          15.90 %= 20.2
