
 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 22:12:27
  [-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=    -530.5852566     RMS force=    0.9815690227E-06
 OPTIM> Final energy  =    -529.8722765     RMS force=    0.9707534666E-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      103.4363533    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2598.2    
 decide> The unconnected minima in the chain and their distances are:
     2       13.64     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=    78
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    209 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    234 steps, energy/image=    -515.0675029     RMS=1.488300309     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   20.65     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 210 RMS= 0.4205 Dev= 1.93% S= 20.68 time= 2.58
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=   9.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     610 steps. Energy=    -532.4532641       time=       1.80
 Minus side of path:                     592 steps. Energy=    -533.2255430       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641  2.6934         -529.7598950  3.4656         -533.2255430   9.333   6.924   9.117  11.736
        *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=     1705.9    
 decide> The unconnected minima in the chain and their distances are:
     2        7.37     3     4       10.83     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=    94
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     58 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     83 steps, energy/image=    -523.6250743     RMS=.6178515288     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   9.367     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4260 Dev= 1.68% S= 8.09 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=   7.95

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     590 steps. Energy=    -530.2320384       time=       1.75
 Minus side of path:                     591 steps. Energy=    -532.4532641       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.2320384 0.49661E-01     -530.1823776  2.2709         -532.4532641   5.780   4.122  23.073   4.637
        *NEW* (Placed in 5)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    49   51 from     0.20643E-01 to     0.21186E-01 ref=     2.3972    
 Connection established between members of the U 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=    96
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    138 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    163 steps, energy/image=    -516.4342567     RMS=.9537261523     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   16.99     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 175 RMS= 0.2926 Dev= 1.80% S= 18.14 time= 1.90
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.23

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     628 steps. Energy=    -532.1827447       time=       1.52
 Minus side of path:                     635 steps. Energy=    -533.2255430       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1827447  2.5111         -529.6716904  3.5539         -533.2255430  16.218  10.550  14.224   7.522
        *NEW* (Placed in 6)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    62   68 from     0.69987E-02 to     0.70514E-02 ref=     3.3767    
 checkperc> Increasing con cutoff atoms    90   95 from     0.15204E-01 to     0.15922E-01 ref=     2.7346    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     430.62    
 decide> The unconnected minima in the chain and their distances are:
     2        5.59     5     6        6.34     1 
 

 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=    97
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -524.2316109     RMS=.2814640822     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   7.350     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.2578 Dev= 0.67% S= 5.77 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     541 steps. Energy=    -530.1820588       time=       1.28
 Minus side of path:                     588 steps. Energy=    -530.2320384       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1820588 0.22917E-01     -530.1591413 0.72897E-01     -530.2320384   4.219   4.073  16.878   6.340
        *NEW* (Placed in 7)                                     Known (#5)
 checkperc> Increasing con cutoff atoms    40   43 from     0.16780E-01 to     0.16799E-01 ref=     2.1663    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 6_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=    95
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     28 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     53 steps, energy/image=    -483.8218651     RMS=17.94128653     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   13.97     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 0.4640 Dev= 0.52% S= 8.01 time= 1.14
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         29
 Converged to TS (number of iterations):         61
 DNEB run yielded 2 true transition state(s) time=   9.90

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     597 steps. Energy=    -530.5852566       time=       1.44
 Minus side of path:                     618 steps. Energy=    -533.2255430       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566 0.59228E-01     -530.5260290  2.6995         -533.2255430   6.553   4.373  22.301   4.798
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     581 steps. Energy=    -532.1046118       time=       1.39
 Minus side of path:                     612 steps. Energy=    -532.1827447       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1046118 0.19346E-01     -532.0852658 0.97479E-01     -532.1827447   3.824   3.582  28.878   3.705
        *NEW* (Placed in 9)                                     Known (#6)
 checkperc> Increasing con cutoff atoms    90   95 from     0.15922E-01 to     0.15949E-01 ref=     2.7346    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     141.12    
 decide> The unconnected minima in the chain and their distances are:
     2        3.67     7     6        4.50     8 
 

 tryconnect> Interpolation for minima 2_F and 7_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=   103
 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=    -524.5024423     RMS=.2891649458     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      2     7 dist=   8.079     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 70 RMS= 0.2023 Dev= 0.54% S= 3.72 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   2.92

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     529 steps. Energy=    -529.8722765       time=       1.25
 Minus side of path:                     591 steps. Energy=    -530.1820588       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8722765 0.22853E-02     -529.8699912 0.31207         -530.1820588   3.759   3.667  15.886   6.736
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> Interpolation for minima 6_F and 8_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=   100
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     22 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     47 steps, energy/image=    -513.7114484     RMS=6.610852095     images=   3
 intlbfgs> First  minimum number      6
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      6     8 dist=   14.48     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      21.82874588    
 Double-ended search iterations= 140 RMS= 0.7908 Dev= 1.38% S= 5.02 time= 1.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.36

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     621 steps. Energy=    -532.1827447       time=       1.51
 Minus side of path:                     617 steps. Energy=    -533.2255430       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1827447  7.9666         -524.2161688  9.0094         -533.2255430   5.335   4.505   7.041  15.196
        Known (#6)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -530.5852566 0.59228E-01    -530.5260290  2.6995        -533.2255430   6.553   4.373  22.301   4.798
   8     -533.2255430  9.0094        -524.2161688  7.9666        -532.1827447   5.335   4.505   7.041  15.196
   3     -532.1827447  2.5111        -529.6716904  3.5539        -533.2255430  16.218  10.550  14.224   7.522
   1     -533.2255430  3.4656        -529.7598950  2.6934        -532.4532641   9.333   6.924   9.117  11.736
   2     -532.4532641  2.2709        -530.1823776 0.49661E-01    -530.2320384   5.780   4.122  23.073   4.637
   4     -530.2320384 0.72897E-01    -530.1591413 0.22917E-01    -530.1820588   4.219   4.073  16.878   6.340
   7     -530.1820588 0.31207        -529.8699912 0.22853E-02    -529.8722765   3.759   3.667  15.886   6.736

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

 Elapsed time=                                76.66
 OPTIM> # of energy calls=                         14 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             19121 time=          38.41 %= 50.1
 OPTIM> # of energy+gradient+Hessian calls=       364 time=          20.28 %= 26.5
