
 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 22:11:40
  [-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=    -451.9866998     RMS force=    0.9559130746E-06
 OPTIM> Final energy  =    -453.6008285     RMS force=    0.9396276176E-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    14   36 from     0.26794E-01 to     0.30048E-01 ref=     2.5125    
 checkperc> Increasing con cutoff atoms    16   26 from     0.11048     to     0.20135     ref=     4.6747    
 checkperc> Increasing con cutoff atoms    16   28 from     0.13416     to     0.24419     ref=     6.7568    
 checkperc> Increasing con cutoff atoms    16   41 from     0.57171E-01 to     0.83237E-01 ref=     4.2048    
 checkperc> Increasing con cutoff atoms    18   22 from     0.56307E-02 to     0.13796E-01 ref=     2.5338    
 checkperc> Increasing con cutoff atoms    18   23 from     0.97630E-02 to     0.28323E-01 ref=     2.8590    
 checkperc> Increasing con cutoff atoms    18   24 from     0.46529E-02 to     0.89201E-02 ref=     3.6846    
 checkperc> Increasing con cutoff atoms    18   25 from     0.82652E-02 to     0.13364E-01 ref=     4.5919    
 checkperc> Increasing con cutoff atoms    18   29 from     0.10534E-01 to     0.13968E-01 ref=     5.4980    
 checkperc> Increasing con cutoff atoms    18   30 from     0.10630E-01 to     0.14357E-01 ref=     6.5749    
 checkperc> Increasing con cutoff atoms    18   31 from     0.12848E-01 to     0.19741E-01 ref=     4.7962    
 checkperc> Increasing con cutoff atoms    18   32 from     0.14109E-01 to     0.23090E-01 ref=     5.5209    
 checkperc> Increasing con cutoff atoms    18   33 from     0.13420E-01 to     0.21151E-01 ref=     3.4055    
 checkperc> Increasing con cutoff atoms    18   34 from     0.17450E-01 to     0.29459E-01 ref=     3.2265    
 checkperc> Increasing con cutoff atoms    18   35 from     0.78118E-02 to     0.99483E-02 ref=     2.6751    
 checkperc> Increasing con cutoff atoms    19   22 from     0.11112     to     0.25288     ref=     2.7392    
 checkperc> Increasing con cutoff atoms    19   24 from     0.55554E-01 to     0.10815     ref=     4.0113    
 checkperc> Increasing con cutoff atoms    19   25 from     0.86028E-01 to     0.17870     ref=     4.8116    
 checkperc> Increasing con cutoff atoms    19   26 from     0.56814E-01 to     0.13525     ref=     4.3852    
 checkperc> Increasing con cutoff atoms    19   27 from     0.88137E-01 to     0.22138     ref=     5.7173    
 checkperc> Increasing con cutoff atoms    19   28 from     0.62740E-01 to     0.15669     ref=     6.5162    
 checkperc> Increasing con cutoff atoms    19   29 from     0.14237     to     0.36540     ref=     6.2254    
 checkperc> Increasing con cutoff atoms    19   30 from     0.14906     to     0.38431     ref=     7.3013    
 checkperc> Increasing con cutoff atoms    19   35 from     0.10669     to     0.26066     ref=     3.4094    
 checkperc> Increasing con cutoff atoms    20   26 from     0.34640E-01 to     0.34857E-01 ref=     4.1540    
 checkperc> Increasing con cutoff atoms    20   36 from     0.91757E-01 to     0.10054     ref=     2.7033    
 checkperc> Increasing con cutoff atoms    21   22 from     0.10682E-02 to     0.17425E-02 ref=     1.3517    
 checkperc> Increasing con cutoff atoms    21   23 from     0.21139E-02 to     0.44969E-02 ref=     2.1642    
 checkperc> Increasing con cutoff atoms    21   24 from     0.26888E-02 to     0.27009E-02 ref=     2.2352    
 checkperc> Increasing con cutoff atoms    22   33 from     0.14967E-02 to     0.15447E-02 ref=     3.6457    
 checkperc> Increasing con cutoff atoms    22   35 from     0.12006E-02 to     0.15727E-02 ref=     2.2454    
 checkperc> Increasing con cutoff atoms    23   24 from     0.23695E-02 to     0.34622E-02 ref=     2.1928    
 checkperc> Increasing con cutoff atoms    23   26 from     0.23527E-02 to     0.26167E-02 ref=     3.3194    
 checkperc> Increasing con cutoff atoms    23   27 from     0.31198E-02 to     0.31825E-02 ref=     4.6675    
 checkperc> Increasing con cutoff atoms    23   29 from     0.24557E-02 to     0.25424E-02 ref=     5.7150    
 checkperc> Increasing con cutoff atoms    26   32 from     0.39662E-02 to     0.40579E-02 ref=     3.8679    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.12867E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    32   35 from     0.30821E-02 to     0.32562E-02 ref=     3.4305    
 checkperc> Increasing con cutoff atoms    33   34 from     0.90799E-03 to     0.10935E-02 ref=     1.0801    
 checkperc> Increasing con cutoff atoms    38   41 from     0.10526E-01 to     0.10902E-01 ref=     2.1024    
 checkperc> Increasing con cutoff atoms    40   52 from     0.19969E-01 to     0.20963E-01 ref=     2.4482    
 checkperc> Increasing con cutoff atoms    40   53 from     0.34446E-01 to     0.37151E-01 ref=     2.5464    
 checkperc> Increasing con cutoff atoms    48   49 from     0.65158E-03 to     0.68339E-03 ref=    0.97632    
 checkperc> Increasing con cutoff atoms    52   58 from     0.98528E-01 to     0.15643     ref=     2.7385    
 checkperc> Increasing con cutoff atoms    52   59 from     0.14828     to     0.20468     ref=     3.0329    
 checkperc> Increasing con cutoff atoms    54   58 from     0.10855E-01 to     0.14072E-01 ref=     2.1512    
 checkperc> Increasing con cutoff atoms    55   57 from     0.87173E-01 to     0.15318     ref=     2.4627    
 checkperc> Increasing con cutoff atoms    55   59 from     0.13385     to     0.19388     ref=     2.8465    
 checkperc> Increasing con cutoff atoms    56   59 from     0.39600E-02 to     0.50381E-02 ref=     1.5031    
 checkperc> Increasing con cutoff atoms    56   64 from     0.14219E-01 to     0.16820E-01 ref=     3.8220    
 checkperc> Increasing con cutoff atoms    56   65 from     0.23278E-01 to     0.25908E-01 ref=     5.1151    
 checkperc> Increasing con cutoff atoms    56   66 from     0.14667E-01 to     0.16778E-01 ref=     5.9818    
 checkperc> Increasing con cutoff atoms    56   67 from     0.41089E-01 to     0.44345E-01 ref=     5.5265    
 checkperc> Increasing con cutoff atoms    56   68 from     0.42211E-01 to     0.45369E-01 ref=     6.6040    
 checkperc> Increasing con cutoff atoms    56   69 from     0.52596E-01 to     0.57327E-01 ref=     4.8334    
 checkperc> Increasing con cutoff atoms    56   70 from     0.58657E-01 to     0.64214E-01 ref=     5.5629    
 checkperc> Increasing con cutoff atoms    56   71 from     0.54997E-01 to     0.60280E-01 ref=     3.4446    
 checkperc> Increasing con cutoff atoms    56   72 from     0.76361E-01 to     0.82488E-01 ref=     3.2822    
 checkperc> Increasing con cutoff atoms    56   73 from     0.27009E-01 to     0.31112E-01 ref=     2.6942    
 checkperc> Increasing con cutoff atoms    57   74 from     0.12234     to     0.15498     ref=     2.7211    
 checkperc> Increasing con cutoff atoms    58   59 from     0.88861E-02 to     0.13541E-01 ref=     2.1155    
 checkperc> Increasing con cutoff atoms    58   74 from     0.11680     to     0.20051     ref=     2.7410    
 checkperc> Increasing con cutoff atoms    59   62 from     0.23722E-02 to     0.57841E-02 ref=     2.2387    
 checkperc> Increasing con cutoff atoms    59   63 from     0.19973E-02 to     0.31917E-02 ref=     3.2016    
 checkperc> Increasing con cutoff atoms    59   74 from     0.30957E-01 to     0.68498E-01 ref=     3.9207    
 checkperc> Increasing con cutoff atoms    60   63 from     0.15459E-02 to     0.23902E-02 ref=     2.1146    
 checkperc> Increasing con cutoff atoms    60   64 from     0.27963E-02 to     0.38541E-02 ref=     2.2804    
 checkperc> Increasing con cutoff atoms    60   65 from     0.43069E-02 to     0.53022E-02 ref=     3.6618    
 checkperc> Increasing con cutoff atoms    60   66 from     0.81439E-02 to     0.94855E-02 ref=     4.1918    
 checkperc> Increasing con cutoff atoms    60   67 from     0.12916E-02 to     0.21698E-02 ref=     4.6475    
 checkperc> Increasing con cutoff atoms    60   68 from     0.23756E-02 to     0.32671E-02 ref=     5.6714    
 checkperc> Increasing con cutoff atoms    61   63 from     0.42105E-02 to     0.58204E-02 ref=     2.5620    
 checkperc> Increasing con cutoff atoms    61   64 from     0.33643E-02 to     0.37981E-02 ref=     3.3175    
 checkperc> Increasing con cutoff atoms    61   65 from     0.61085E-02 to     0.64040E-02 ref=     4.6637    
 checkperc> Increasing con cutoff atoms    61   66 from     0.11505E-01 to     0.12095E-01 ref=     5.0771    
 checkperc> Increasing con cutoff atoms    61   67 from     0.20209E-02 to     0.25438E-02 ref=     5.7140    
 checkperc> Increasing con cutoff atoms    61   68 from     0.35699E-02 to     0.38017E-02 ref=     6.7229    
 checkperc> Increasing con cutoff atoms    62   63 from     0.45031E-03 to     0.16684E-02 ref=     1.0146    
 checkperc> Increasing con cutoff atoms    62   66 from     0.84054E-02 to     0.94776E-02 ref=     2.8853    
 checkperc> Increasing con cutoff atoms    62   71 from     0.15035E-02 to     0.29067E-02 ref=     3.5435    
 checkperc> Increasing con cutoff atoms    62   72 from     0.61252E-02 to     0.82900E-02 ref=     4.3826    
 checkperc> Increasing con cutoff atoms    62   73 from     0.26790E-02 to     0.57885E-02 ref=     2.2214    
 checkperc> Increasing con cutoff atoms    63   64 from     0.11887E-02 to     0.19930E-02 ref=     2.1308    
 checkperc> Increasing con cutoff atoms    63   72 from     0.50132E-02 to     0.55564E-02 ref=     5.3618    
 checkperc> Increasing con cutoff atoms    63   73 from     0.29388E-02 to     0.49980E-02 ref=     3.2079    
 checkperc> Increasing con cutoff atoms    64   73 from     0.18847E-02 to     0.25320E-02 ref=     1.4297    
 checkperc> Increasing con cutoff atoms    64   74 from     0.13005     to     0.22124     ref=     6.1419    
 checkperc> Increasing con cutoff atoms    65   66 from     0.10858E-03 to     0.56929E-03 ref=     1.0812    
 checkperc> Increasing con cutoff atoms    66   73 from     0.40538E-02 to     0.41215E-02 ref=     3.4590    
 checkperc> Increasing con cutoff atoms   116  117 from     0.10843E-02 to     0.10864E-02 ref=     1.0916    
 initialise> Interpolation metric value for minima 1 and 2 is      25.95261106    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     17235.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.80     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=   132
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     89 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    114 steps, energy/image=    -425.4443713     RMS=1.984283030     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   30.39     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0484 Dev= 1.77% S= 27.71 time= 21.34
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  25.13

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1234 steps. Energy=    -451.9866998       time=      13.81
 Minus side of path:                    1308 steps. Energy=    -453.6008285       time=      15.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.9866998  1.0762         -450.9104840  2.6903         -453.6008285  27.705  25.857   6.657  32.748
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -451.9866998  1.0762        -450.9104840  2.6903        -453.6008285  27.705  25.857   6.657  32.748

 Number of TS in the path       =      1
 Number of cycles               =      1

 Elapsed time=                                76.68
 OPTIM> # of energy calls=                          2 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=              6710 time=          49.93 %= 65.1
 OPTIM> # of energy+gradient+Hessian calls=        24 time=           7.02 %=  9.2
