
 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 22:17:55
  [-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=    -532.9755405     RMS force=    0.9407827642E-06
 OPTIM> Final energy  =    -538.0921206     RMS force=    0.9888668241E-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      102.4675528    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2371.6    
 decide> The unconnected minima in the chain and their distances are:
     2       13.23     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=    81
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    285 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    310 steps, energy/image=    -511.6188234     RMS=1.003397453     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   19.79     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2926 Dev= 1.97% S= 21.31 time= 1.79
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         40
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=   8.41

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     622 steps. Energy=    -533.6478626       time=       1.53
 Minus side of path:                     778 steps. Energy=    -533.9897019       time=       2.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.6478626  3.5587         -530.0891765  3.9005         -533.9897019  17.463  13.510   4.514  23.703
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    65   66 from     0.16276E-02 to     0.17251E-02 ref=     1.2274    
 checkperc> Increasing con cutoff atoms    90   93 from     0.38216E-02 to     0.39128E-02 ref=     1.5207    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     631 steps. Energy=    -535.4215294       time=       1.57
 Minus side of path:                     730 steps. Energy=    -539.7280952       time=       1.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4215294  4.6631         -530.7584009  8.9697         -539.7280952  14.720   9.851   4.919  21.751
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms     1    8 from     0.12374E-01 to     0.12832E-01 ref=     2.4907    
 checkperc> Increasing con cutoff atoms     2   12 from     0.14452     to     0.14728     ref=     5.6993    
 checkperc> Increasing con cutoff atoms    13   16 from     0.13428E-01 to     0.14355E-01 ref=     3.0447    
 checkperc> Increasing con cutoff atoms    90   93 from     0.39128E-02 to     0.40725E-02 ref=     1.5207    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     3303.8    
 decide> The unconnected minima in the chain and their distances are:
     2       14.11     6     5        4.44     4     3        7.34     1 
 

 tryconnect> Interpolation for minima 2_F 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=    76
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    111 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    136 steps, energy/image=    -529.6135518     RMS=.7246970732     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   17.74     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.0894 Dev= 1.03% S= 15.11 time= 1.79
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.74

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     768 steps. Energy=    -538.1436644       time=       2.07
 Minus side of path:                     675 steps. Energy=    -539.7280952       time=       1.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.1436644 0.69867         -537.4449909  2.2831         -539.7280952  18.914  14.031   5.371  19.921
        *NEW* (Placed in 7)                                     Known (#6)
 checkperc> Increasing con cutoff atoms     2    5 from     0.30562E-02 to     0.30778E-02 ref=     2.0610    
 checkperc> Increasing con cutoff atoms     2    8 from     0.10982E-01 to     0.11107E-01 ref=     3.3648    
 checkperc> Increasing con cutoff atoms     5   10 from     0.76105E-02 to     0.78055E-02 ref=     2.4430    
 checkperc> Increasing con cutoff atoms     5   11 from     0.19782E-01 to     0.22390E-01 ref=     2.5503    
 checkperc> Increasing con cutoff atoms    13   16 from     0.14355E-01 to     0.15090E-01 ref=     3.0447    
 checkperc> Increasing con cutoff atoms    89   90 from     0.17936E-01 to     0.18490E-01 ref=     2.1366    
 checkperc> Increasing con cutoff atoms    91   93 from     0.20308E-01 to     0.21383E-01 ref=     2.1253    
 checkperc> Increasing con cutoff atoms    91   98 from     0.54437E-01 to     0.58704E-01 ref=     4.7863    
 checkperc> Increasing con cutoff atoms    91   99 from     0.63604E-01 to     0.66932E-01 ref=     6.1213    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 4_U 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=   103
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     56 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     81 steps, energy/image=    -528.3282201     RMS=.1313379536     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   5.948     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2324 Dev= 0.21% S= 4.91 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   3.01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     830 steps. Energy=    -533.9897019       time=       2.43
 Minus side of path:                     631 steps. Energy=    -535.4215294       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9897019 0.54445         -533.4452505  1.9763         -535.4215294   5.640   4.444  25.270   4.234
        Known (#4)                                              Known (#5)
 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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     36 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     61 steps, energy/image=    -496.1749289     RMS=12.55749497     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   15.28     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 140 RMS= 0.4545 Dev= 1.41% S= 8.18 time= 1.18
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  12.28

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     630 steps. Energy=    -533.5544476       time=       1.67
 Minus side of path:                     748 steps. Energy=    -532.9755405       time=       1.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5544476  1.5478         -532.0066527 0.96889         -532.9755405  19.836  17.142   7.431  14.398
        *NEW* (Placed in 8)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    10   15 from     0.94316E-01 to     0.99927E-01 ref=     2.6487    
 checkperc> Increasing con cutoff atoms    42   43 from     0.18842E-02 to     0.19034E-02 ref=     1.0902    
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     974.51    
 decide> The unconnected minima in the chain and their distances are:
     2        5.67     7     3        7.34     1 
 

 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=   100
 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=    -532.6871002     RMS=.1175649363     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      2     7 dist=   13.27     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 0.1361 Dev= 1.20% S= 5.74 time= 0.65
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.00

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     566 steps. Energy=    -538.0921206       time=       1.35
 Minus side of path:                     672 steps. Energy=    -538.1436644       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0921206 0.32936E-02     -538.0888271 0.54837E-01     -538.1436644   5.759   5.668  11.422   9.368
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     31 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     56 steps, energy/image=    -490.6215116     RMS=10.48876293     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   16.54     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0147 Dev= 6.23% S= 10.30 time= 37.72
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.18

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     603 steps. Energy=    -532.9755405       time=       1.48
 Minus side of path:                     642 steps. Energy=    -533.6478626       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9755405  9.2285         -523.7470891  9.9008         -533.6478626   7.766   7.336   4.533  23.607
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -532.9755405  9.2285        -523.7470891  9.9008        -533.6478626   7.766   7.336   4.533  23.607
   1     -533.6478626  3.5587        -530.0891765  3.9005        -533.9897019  17.463  13.510   4.514  23.703
   4     -533.9897019 0.54445        -533.4452505  1.9763        -535.4215294   5.640   4.444  25.270   4.234
   2     -535.4215294  4.6631        -530.7584009  8.9697        -539.7280952  14.720   9.851   4.919  21.751
   3     -539.7280952  2.2831        -537.4449909 0.69867        -538.1436644  18.914  14.031   5.371  19.921
   6     -538.1436644 0.54837E-01    -538.0888271 0.32936E-02    -538.0921206   5.759   5.668  11.422   9.368

 Number of TS in the path       =      6
 Number of cycles               =      3

 Elapsed time=                               104.77
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             36578 time=          73.18 %= 69.9
 OPTIM> # of energy+gradient+Hessian calls=       266 time=          15.00 %= 14.3
