
 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 22:16:48
  [-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=    -529.6554571     RMS force=    0.9668610016E-06
 OPTIM> Final energy  =    -539.6623457     RMS force=    0.8397805913E-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      61.59127162    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     73898.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.90     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=     8
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    575 fraction=    0.990000 images=     6 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    600 steps, energy/image=     1133.003207     RMS=32.50425592     images=   7
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   49.22     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0846 Dev= 3.86% S= 54.69 time= 13.96
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     636 steps. Energy=    -527.5267375       time=       1.55
 Minus side of path:                     831 steps. Energy=    -537.4922044       time=       2.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.5267375 0.23195         -527.2947865  10.197         -537.4922044  29.267  27.302   2.123  50.389
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    59   62 from     0.44048E-02 to     0.44551E-02 ref=     1.5397    
 checkperc> Increasing con cutoff atoms    88  106 from     0.19578E-01 to     0.20982E-01 ref=     2.4212    
 checkperc> Increasing con cutoff atoms    90   97 from     0.12638E-01 to     0.13184E-01 ref=     4.7038    
 checkperc> Increasing con cutoff atoms    98  104 from     0.52649E-02 to     0.53288E-02 ref=     3.4225    
 checkperc> Increasing con cutoff atoms     1    8 from     0.14100E-01 to     0.14204E-01 ref=     2.4881    
 checkperc> Increasing con cutoff atoms     5   11 from     0.17769E-01 to     0.18257E-01 ref=     2.5525    
 checkperc> Increasing con cutoff atoms    10   11 from     0.40699E-02 to     0.47976E-02 ref=     1.0152    
 checkperc> Increasing con cutoff atoms    10   17 from     0.23519E-01 to     0.25700E-01 ref=     3.8324    
 checkperc> Increasing con cutoff atoms    11   12 from     0.11013E-01 to     0.12256E-01 ref=     2.1353    
 checkperc> Increasing con cutoff atoms    13   26 from     0.55805E-01 to     0.56968E-01 ref=     4.0088    
 checkperc> Increasing con cutoff atoms    24   28 from     0.31624E-01 to     0.32143E-01 ref=     2.4467    
 checkperc> Increasing con cutoff atoms    27   28 from     0.19695E-01 to     0.19919E-01 ref=     2.1303    
 checkperc> Increasing con cutoff atoms    29   31 from     0.14381E-01 to     0.14845E-01 ref=     2.1461    
 checkperc> Increasing con cutoff atoms    88  107 from     0.20583E-01 to     0.23393E-01 ref=     2.4161    
 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=     7366.6    
 decide> The unconnected minima in the chain and their distances are:
     2       10.20     4     3       18.45     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=    90
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     39 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     64 steps, energy/image=    -531.8521236     RMS=.2938860942     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   11.24     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.1153 Dev= 0.57% S= 10.65 time= 0.65
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.16

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     563 steps. Energy=    -538.7028350       time=       1.37
 Minus side of path:                     570 steps. Energy=    -537.4922044       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.7028350  1.3656         -537.3372527 0.15495         -537.4922044   6.513   5.661  19.410   5.513
        *NEW* (Placed in 5)                                     Known (#4)
 checkperc> Increasing con cutoff atoms     2    4 from     0.48622E-02 to     0.74601E-02 ref=     1.6414    
 checkperc> Increasing con cutoff atoms     2    6 from     0.20285E-01 to     0.25484E-01 ref=     2.4129    
 checkperc> Increasing con cutoff atoms     3    6 from     0.21142E-01 to     0.27130E-01 ref=     2.4074    
 checkperc> Increasing con cutoff atoms     3    7 from     0.21366E-01 to     0.23446E-01 ref=     2.4034    
 checkperc> Increasing con cutoff atoms     4    6 from     0.34742E-02 to     0.51765E-02 ref=     2.9545    
 checkperc> Increasing con cutoff atoms     4    7 from     0.19343E-01 to     0.31970E-01 ref=     2.4145    
 checkperc> Increasing con cutoff atoms     8   10 from     0.20372E-02 to     0.21530E-02 ref=     1.3374    
 checkperc> Increasing con cutoff atoms    88  107 from     0.23393E-01 to     0.28260E-01 ref=     2.4161    
 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=    47
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     79 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    104 steps, energy/image=    -490.5926120     RMS=18.66787354     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   25.43     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 245 RMS= 2.1035 Dev= 1.36% S= 19.37 time= 3.50
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.73

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     617 steps. Energy=    -527.5267375       time=       1.51
 Minus side of path:                     722 steps. Energy=    -530.8886546       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.5267375 0.94550E-01     -527.4321874  3.4565         -530.8886546  17.809  17.137   2.645  40.457
        Known (#3)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms     1    3 from     0.39058E-03 to     0.39822E-03 ref=     1.0081    
 checkperc> Increasing con cutoff atoms     1    4 from     0.24503E-02 to     0.24525E-02 ref=     1.0104    
 checkperc> Increasing con cutoff atoms     2    7 from     0.42727E-02 to     0.42883E-02 ref=     2.9555    
 checkperc> Increasing con cutoff atoms    13   28 from     0.14460     to     0.14972     ref=     4.6557    
 checkperc> Increasing con cutoff atoms    19   21 from     0.41680E-02 to     0.42064E-02 ref=     1.0134    
 checkperc> Increasing con cutoff atoms    24   27 from     0.19883E-01 to     0.21275E-01 ref=     2.0781    
 checkperc> Increasing con cutoff atoms    72   76 from     0.39426E-01 to     0.39533E-01 ref=     2.4666    
 checkperc> Increasing con cutoff atoms    76   77 from     0.13411E-02 to     0.13461E-02 ref=     1.0901    
 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=     827.93    
 decide> The unconnected minima in the chain and their distances are:
     2        8.75     5     6        5.37     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=    90
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     18 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     43 steps, energy/image=    -517.4185072     RMS=10.20366289     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   15.78     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.0845 Dev= 0.17% S= 9.00 time= 1.15
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        125
 DNEB run yielded 1 true transition state(s) time=  11.93

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     607 steps. Energy=    -539.6623457       time=       1.49
 Minus side of path:                     537 steps. Energy=    -538.7028350       time=       1.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -539.6623457  1.1932         -538.4691953 0.23364         -538.7028350   9.486   8.756   7.209  14.842
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 6_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=   101
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     37 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     62 steps, energy/image=    -509.1443982     RMS=20.27430693     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   15.53     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 140 RMS= 0.2157 Dev= 0.54% S= 5.63 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     594 steps. Energy=    -529.6554571       time=       1.45
 Minus side of path:                     626 steps. Energy=    -530.8886546       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.6554571 0.44458         -529.2108807  1.6778         -530.8886546   5.846   5.374  11.398   9.388
        Known (#1)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -529.6554571 0.44458        -529.2108807  1.6778        -530.8886546   5.846   5.374  11.398   9.388
   3     -530.8886546  3.4565        -527.4321874 0.94550E-01    -527.5267375  17.809  17.137   2.645  40.457
   1     -527.5267375 0.23195        -527.2947865  10.197        -537.4922044  29.267  27.302   2.123  50.389
   2     -537.4922044 0.15495        -537.3372527  1.3656        -538.7028350   6.513   5.661  19.410   5.513
   4     -538.7028350 0.23364        -538.4691953  1.1932        -539.6623457   9.486   8.756   7.209  14.842

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                                68.94
 OPTIM> # of energy calls=                         10 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             20118 time=          40.11 %= 58.2
 OPTIM> # of energy+gradient+Hessian calls=       295 time=          16.27 %= 23.6
