
 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 22:14:32
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 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=    25
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>  654 Cartesian coordinates will be optimised for  218 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=    -452.9989322     RMS force=    0.8683591470E-06
 OPTIM> Final energy  =    -452.5935588     RMS force=    0.9386933433E-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

 checkperc> Increasing con cutoff atoms    20   35 from     0.78073E-01 to     0.78392E-01 ref=     2.8522    
 checkperc> Increasing con cutoff atoms    20   36 from     0.91757E-01 to     0.96114E-01 ref=     2.7033    
 checkperc> Increasing con cutoff atoms    21   29 from     0.29683E-02 to     0.29938E-02 ref=     4.2912    
 checkperc> Increasing con cutoff atoms    22   29 from     0.20120E-02 to     0.27157E-02 ref=     4.6479    
 checkperc> Increasing con cutoff atoms    22   31 from     0.27977E-02 to     0.32580E-02 ref=     4.6345    
 checkperc> Increasing con cutoff atoms    22   32 from     0.37553E-02 to     0.40932E-02 ref=     5.6545    
 checkperc> Increasing con cutoff atoms    23   29 from     0.24557E-02 to     0.26659E-02 ref=     5.7150    
 checkperc> Increasing con cutoff atoms    23   31 from     0.26455E-02 to     0.31243E-02 ref=     5.7145    
 checkperc> Increasing con cutoff atoms    23   32 from     0.35633E-02 to     0.38950E-02 ref=     6.7255    
 checkperc> Increasing con cutoff atoms    26   27 from     0.81021E-03 to     0.86629E-03 ref=     1.4030    
 checkperc> Increasing con cutoff atoms    26   29 from     0.12154E-02 to     0.14806E-02 ref=     2.4216    
 checkperc> Increasing con cutoff atoms    29   34 from     0.14292E-02 to     0.15138E-02 ref=     3.4183    
 checkperc> Increasing con cutoff atoms    29   35 from     0.17678E-02 to     0.22965E-02 ref=     2.8542    
 checkperc> Increasing con cutoff atoms    30   34 from     0.21544E-02 to     0.24439E-02 ref=     4.3093    
 checkperc> Increasing con cutoff atoms    30   35 from     0.21851E-02 to     0.25569E-02 ref=     3.9362    
 checkperc> Increasing con cutoff atoms    31   33 from     0.85966E-03 to     0.89525E-03 ref=     1.4086    
 checkperc> Increasing con cutoff atoms    31   34 from     0.17415E-02 to     0.23749E-02 ref=     2.1569    
 checkperc> Increasing con cutoff atoms    31   35 from     0.21128E-02 to     0.23886E-02 ref=     2.4568    
 checkperc> Increasing con cutoff atoms    32   33 from     0.21779E-02 to     0.22129E-02 ref=     2.1594    
 checkperc> Increasing con cutoff atoms    32   34 from     0.30298E-02 to     0.41983E-02 ref=     2.4783    
 checkperc> Increasing con cutoff atoms    32   35 from     0.30821E-02 to     0.33841E-02 ref=     3.4305    
 checkperc> Increasing con cutoff atoms    40   48 from     0.26768E-01 to     0.27974E-01 ref=     2.4207    
 checkperc> Increasing con cutoff atoms    40   50 from     0.59134E-02 to     0.61716E-02 ref=     1.5314    
 checkperc> Increasing con cutoff atoms    40   55 from     0.42108E-01 to     0.10794     ref=     4.1623    
 checkperc> Increasing con cutoff atoms    50   51 from     0.23503E-02 to     0.32722E-02 ref=     1.2317    
 checkperc> Increasing con cutoff atoms    52   56 from     0.19935E-01 to     0.24676E-01 ref=     2.4622    
 checkperc> Increasing con cutoff atoms    52   74 from     0.38440E-01 to     0.61743E-01 ref=     2.4800    
 checkperc> Increasing con cutoff atoms    54   74 from     0.52104E-02 to     0.53981E-02 ref=     1.5431    
 checkperc> Increasing con cutoff atoms    54   75 from     0.10156E-01 to     0.10267E-01 ref=     2.4176    
 checkperc> Increasing con cutoff atoms    55   74 from     0.11909E-01 to     0.20816E-01 ref=     2.1468    
 checkperc> Increasing con cutoff atoms    55   75 from     0.11111     to     0.13577     ref=     3.1640    
 checkperc> Increasing con cutoff atoms    55   76 from     0.14433     to     0.14728     ref=     2.6292    
 checkperc> Increasing con cutoff atoms    56   74 from     0.32724E-01 to     0.38937E-01 ref=     2.5401    
 checkperc> Increasing con cutoff atoms    57   58 from     0.35460E-02 to     0.56518E-02 ref=     1.7538    
 checkperc> Increasing con cutoff atoms    59   72 from     0.22220E-01 to     0.23164E-01 ref=     2.9915    
 checkperc> Increasing con cutoff atoms    60   72 from     0.15314E-01 to     0.15769E-01 ref=     4.2035    
 checkperc> Increasing con cutoff atoms    62   72 from     0.61252E-02 to     0.69365E-02 ref=     4.3826    
 checkperc> Increasing con cutoff atoms    71   73 from     0.17041E-02 to     0.21545E-02 ref=     1.4149    
 checkperc> Increasing con cutoff atoms    72   73 from     0.39601E-02 to     0.45761E-02 ref=     2.1615    
 checkperc> Increasing con cutoff atoms    74   76 from     0.16946E-02 to     0.28178E-02 ref=     1.3379    
 checkperc> Increasing con cutoff atoms    74   77 from     0.67716E-02 to     0.12164E-01 ref=     2.0201    
 checkperc> Increasing con cutoff atoms    75   77 from     0.82756E-02 to     0.87473E-02 ref=     3.1370    
 checkperc> Increasing con cutoff atoms    76   77 from     0.22231E-02 to     0.42417E-02 ref=     1.0122    
 checkperc> Increasing con cutoff atoms    76   78 from     0.31434E-02 to     0.49696E-02 ref=     1.4714    
 checkperc> Increasing con cutoff atoms    76   89 from     0.36085E-01 to     0.43158E-01 ref=     2.4925    
 initialise> Interpolation metric value for minima 1 and 2 is      38.15526840    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     54910.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.97     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=    50
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    262 fraction=    0.990000 images=     4 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    287 steps, energy/image=    -441.3670667     RMS=1.962834981     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   41.79     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0832 Dev= 0.59% S= 40.68 time= 38.35
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=  50.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1474 steps. Energy=    -452.9989322       time=      17.86
 Minus side of path:                    1650 steps. Energy=    -454.6876445       time=      20.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9989322 0.99332         -452.0056076  2.6820         -454.6876445  53.876  49.875   2.850  76.482
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    21   30 from     0.29937E-02 to     0.37977E-02 ref=     5.3715    
 checkperc> Increasing con cutoff atoms    26   33 from     0.12466E-02 to     0.15130E-02 ref=     2.4209    
 checkperc> Increasing con cutoff atoms    27   29 from     0.53012E-03 to     0.61641E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    27   30 from     0.15137E-02 to     0.20082E-02 ref=     2.1611    
 checkperc> Increasing con cutoff atoms    29   30 from     0.77416E-03 to     0.10489E-02 ref=     1.0823    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.15264E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    29   35 from     0.22965E-02 to     0.24734E-02 ref=     2.8542    
 checkperc> Increasing con cutoff atoms    30   31 from     0.15610E-02 to     0.16675E-02 ref=     2.1624    
 checkperc> Increasing con cutoff atoms    30   33 from     0.16402E-02 to     0.23751E-02 ref=     3.4241    
 checkperc> Increasing con cutoff atoms    30   35 from     0.25569E-02 to     0.33682E-02 ref=     3.9362    
 checkperc> Increasing con cutoff atoms    41   42 from     0.11067E-01 to     0.11508E-01 ref=     2.1405    
 checkperc> Increasing con cutoff atoms    41   44 from     0.65831E-01 to     0.77192E-01 ref=     2.6830    
 checkperc> Increasing con cutoff atoms    41   46 from     0.41533E-01 to     0.49390E-01 ref=     3.6833    
 checkperc> Increasing con cutoff atoms    45   47 from     0.23345E-02 to     0.24619E-02 ref=     1.7767    
 checkperc> Increasing con cutoff atoms    80   85 from     0.12183E-01 to     0.12403E-01 ref=     2.1523    
 checkperc> Increasing con cutoff atoms   112  116 from     0.39849E-01 to     0.40508E-01 ref=     2.4441    
 checkperc> Increasing con cutoff atoms   116  117 from     0.10843E-02 to     0.10997E-02 ref=     1.0916    
 checkperc> Increasing con cutoff atoms   127  129 from     0.79792E-01 to     0.80636E-01 ref=     2.4190    
 checkperc> Increasing con cutoff atoms   127  131 from     0.94113E-02 to     0.96177E-02 ref=     2.9751    
 checkperc> Increasing con cutoff atoms   128  130 from     0.60812E-02 to     0.60864E-02 ref=     1.0157    
 checkperc> Increasing con cutoff atoms   129  131 from     0.11318E-01 to     0.11379E-01 ref=     1.6381    
 checkperc> Increasing con cutoff atoms   149  153 from     0.18695E-02 to     0.21141E-02 ref=     2.4442    
 checkperc> Increasing con cutoff atoms   174  194 from     0.63182E-02 to     0.63537E-02 ref=     1.5453    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     37650.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.48     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=    69
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    163 fraction=    0.990000 images=     3 time=       0.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    188 steps, energy/image=    -421.9432463     RMS=12.66468656     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   37.48     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0161 Dev= 1.33% S= 35.00 time= 31.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  26.56

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1221 steps. Energy=    -452.5935588       time=      13.51
 Minus side of path:                    1590 steps. Energy=    -454.9365419       time=      19.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.5935588 0.58045E-01     -452.5355136  2.4010         -454.9365419  34.680  33.426   2.807  77.656
        Known (#2)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     40920.    
 decide> The unconnected minima in the chain and their distances are:
     4       34.43     3 
 

 tryconnect> Interpolation for minima 3_S and 4_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=    72
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    305 fraction=    0.990000 images=     5 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    330 steps, energy/image=     30.33627440     RMS=20.80376526     images=   5
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   46.31     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 455 RMS= 0.0255 Dev= 0.32% S= 35.20 time= 43.78
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=  20.92

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1234 steps. Energy=    -454.6876445       time=      12.46
 Minus side of path:                    1222 steps. Energy=    -454.9365419       time=      12.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.6876445 0.29106         -454.3965829 0.53996         -454.9365419  36.123  34.472   3.182  68.504
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -452.9989322 0.99332        -452.0056076  2.6820        -454.6876445  53.876  49.875   2.850  76.482
   3     -454.6876445 0.29106        -454.3965829 0.53996        -454.9365419  36.123  34.472   3.182  68.504
   2     -454.9365419  2.4010        -452.5355136 0.58045E-01    -452.5935588  34.680  33.426   2.807  77.656

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

 Elapsed time=                               312.44
 OPTIM> # of energy calls=                          6 time=           0.05 %=  0.0
 OPTIM> # of energy+gradient calls=             27536 time=         203.31 %= 65.1
 OPTIM> # of energy+gradient+Hessian calls=       142 time=          40.84 %= 13.1
