
 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 22:09:48
  [-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 = 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=    -450.5501243     RMS force=    0.9377998691E-06
 OPTIM> Final energy  =    -449.3924540     RMS force=    0.9414074045E-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     1    2 from     0.38670E-03 to     0.40939E-03 ref=     1.0090    
 checkperc> Increasing con cutoff atoms     2    3 from     0.81702E-02 to     0.81986E-02 ref=     1.6437    
 checkperc> Increasing con cutoff atoms     2    6 from     0.12253E-02 to     0.13588E-02 ref=     2.9470    
 checkperc> Increasing con cutoff atoms     3    6 from     0.19686E-01 to     0.19932E-01 ref=     2.3742    
 checkperc> Increasing con cutoff atoms     4    5 from     0.95559E-02 to     0.96491E-02 ref=     2.0605    
 checkperc> Increasing con cutoff atoms     4    7 from     0.37467E-01 to     0.37550E-01 ref=     2.6633    
 checkperc> Increasing con cutoff atoms     5    9 from     0.59700E-02 to     0.60070E-02 ref=     2.1642    
 checkperc> Increasing con cutoff atoms     6    7 from     0.69386E-02 to     0.70587E-02 ref=     2.1294    
 checkperc> Increasing con cutoff atoms     6   12 from     0.94948E-02 to     0.96777E-02 ref=     2.1259    
 checkperc> Increasing con cutoff atoms     7    9 from     0.23845E-03 to     0.24877E-03 ref=     1.0920    
 checkperc> Increasing con cutoff atoms     9   11 from     0.61001E-01 to     0.61446E-01 ref=     2.2570    
 checkperc> Increasing con cutoff atoms    13   15 from     0.37592E-02 to     0.42186E-02 ref=     3.1433    
 checkperc> Increasing con cutoff atoms    14   15 from     0.35264E-02 to     0.36668E-02 ref=     1.0147    
 checkperc> Increasing con cutoff atoms    16   19 from     0.76980E-02 to     0.87755E-02 ref=     2.1572    
 checkperc> Increasing con cutoff atoms    17   21 from     0.89021E-01 to     0.11850     ref=     2.7732    
 checkperc> Increasing con cutoff atoms    18   22 from     0.56307E-02 to     0.87070E-02 ref=     2.5338    
 checkperc> Increasing con cutoff atoms    18   23 from     0.97630E-02 to     0.18307E-01 ref=     2.8590    
 checkperc> Increasing con cutoff atoms    18   26 from     0.50240E-02 to     0.76221E-02 ref=     3.8121    
 checkperc> Increasing con cutoff atoms    18   27 from     0.69953E-02 to     0.13857E-01 ref=     5.0991    
 checkperc> Increasing con cutoff atoms    18   28 from     0.70737E-02 to     0.10621E-01 ref=     5.9699    
 checkperc> Increasing con cutoff atoms    18   29 from     0.10534E-01 to     0.19619E-01 ref=     5.4980    
 checkperc> Increasing con cutoff atoms    18   30 from     0.10630E-01 to     0.20259E-01 ref=     6.5749    
 checkperc> Increasing con cutoff atoms    18   31 from     0.12848E-01 to     0.23908E-01 ref=     4.7962    
 checkperc> Increasing con cutoff atoms    18   32 from     0.14109E-01 to     0.27083E-01 ref=     5.5209    
 checkperc> Increasing con cutoff atoms    18   33 from     0.13420E-01 to     0.24614E-01 ref=     3.4055    
 checkperc> Increasing con cutoff atoms    18   34 from     0.17450E-01 to     0.31917E-01 ref=     3.2265    
 checkperc> Increasing con cutoff atoms    18   35 from     0.78118E-02 to     0.13267E-01 ref=     2.6751    
 checkperc> Increasing con cutoff atoms    19   21 from     0.16310E-01 to     0.20550E-01 ref=     2.1099    
 checkperc> Increasing con cutoff atoms    19   26 from     0.56814E-01 to     0.57840E-01 ref=     4.3852    
 checkperc> Increasing con cutoff atoms    19   28 from     0.62740E-01 to     0.65551E-01 ref=     6.5162    
 checkperc> Increasing con cutoff atoms    20   36 from     0.91757E-01 to     0.10867     ref=     2.7033    
 checkperc> Increasing con cutoff atoms    21   27 from     0.25193E-02 to     0.35007E-02 ref=     3.6897    
 checkperc> Increasing con cutoff atoms    21   33 from     0.30076E-02 to     0.30994E-02 ref=     2.6548    
 checkperc> Increasing con cutoff atoms    21   34 from     0.44130E-02 to     0.54822E-02 ref=     2.9736    
 checkperc> Increasing con cutoff atoms    22   34 from     0.29040E-02 to     0.31271E-02 ref=     4.1911    
 checkperc> Increasing con cutoff atoms    23   34 from     0.36344E-02 to     0.45789E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    24   29 from     0.20320E-02 to     0.30599E-02 ref=     3.7645    
 checkperc> Increasing con cutoff atoms    24   30 from     0.25681E-02 to     0.34846E-02 ref=     4.6887    
 checkperc> Increasing con cutoff atoms    24   31 from     0.29172E-02 to     0.31288E-02 ref=     4.1390    
 checkperc> Increasing con cutoff atoms    24   32 from     0.42558E-02 to     0.44417E-02 ref=     5.2173    
 checkperc> Increasing con cutoff atoms    26   29 from     0.12154E-02 to     0.21992E-02 ref=     2.4216    
 checkperc> Increasing con cutoff atoms    26   30 from     0.18611E-02 to     0.24399E-02 ref=     3.4056    
 checkperc> Increasing con cutoff atoms    26   31 from     0.25343E-02 to     0.36711E-02 ref=     2.7870    
 checkperc> Increasing con cutoff atoms    26   32 from     0.39662E-02 to     0.51280E-02 ref=     3.8679    
 checkperc> Increasing con cutoff atoms    26   35 from     0.78530E-03 to     0.12585E-02 ref=     1.4283    
 checkperc> Increasing con cutoff atoms    27   28 from     0.12483E-02 to     0.19314E-02 ref=     1.0804    
 checkperc> Increasing con cutoff atoms    27   33 from     0.19684E-02 to     0.28844E-02 ref=     2.8210    
 checkperc> Increasing con cutoff atoms    27   34 from     0.20580E-02 to     0.25016E-02 ref=     3.9013    
 checkperc> Increasing con cutoff atoms    27   35 from     0.19455E-02 to     0.40841E-02 ref=     2.4820    
 checkperc> Increasing con cutoff atoms    28   31 from     0.25380E-02 to     0.26371E-02 ref=     3.4147    
 checkperc> Increasing con cutoff atoms    28   33 from     0.29113E-02 to     0.46576E-02 ref=     3.9012    
 checkperc> Increasing con cutoff atoms    28   34 from     0.28671E-02 to     0.44231E-02 ref=     4.9817    
 checkperc> Increasing con cutoff atoms    28   35 from     0.34501E-02 to     0.45963E-02 ref=     3.4544    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.17985E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    78   79 from     0.10006E-02 to     0.10282E-02 ref=     1.0907    
 checkperc> Increasing con cutoff atoms    98  101 from     0.81536E-02 to     0.88659E-02 ref=     2.0112    
 checkperc> Increasing con cutoff atoms    99  100 from     0.46533E-02 to     0.72905E-02 ref=     2.2070    
 checkperc> Increasing con cutoff atoms    99  101 from     0.14044E-01 to     0.22216E-01 ref=     2.4249    
 checkperc> Increasing con cutoff atoms   101  102 from     0.69819E-02 to     0.83135E-02 ref=     1.7575    
 checkperc> Increasing con cutoff atoms   107  112 from     0.27836E-01 to     0.28325E-01 ref=     2.4549    
 checkperc> Increasing con cutoff atoms   107  113 from     0.55015E-01 to     0.55110E-01 ref=     2.5502    
 checkperc> Increasing con cutoff atoms   108  110 from     0.13782E-01 to     0.14678E-01 ref=     2.1303    
 checkperc> Increasing con cutoff atoms   110  112 from     0.34830E-02 to     0.36073E-02 ref=     1.3378    
 checkperc> Increasing con cutoff atoms   164  167 from     0.10122E-02 to     0.10188E-02 ref=     1.0894    
 checkperc> Increasing con cutoff atoms   182  183 from     0.27373E-02 to     0.29347E-02 ref=     1.0161    
 checkperc> Increasing con cutoff atoms   183  184 from     0.60336E-02 to     0.61416E-02 ref=     2.1326    
 checkperc> Increasing con cutoff atoms   184  187 from     0.14406E-02 to     0.19584E-02 ref=     2.4219    
 checkperc> Increasing con cutoff atoms   184  188 from     0.25062E-02 to     0.32039E-02 ref=     3.4054    
 checkperc> Increasing con cutoff atoms   187  188 from     0.87971E-03 to     0.10267E-02 ref=     1.0821    
 initialise> Interpolation metric value for minima 1 and 2 is      18.04155210    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     5889.2    
 decide> The unconnected minima in the chain and their distances are:
     2       18.04     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=   135
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     85 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    110 steps, energy/image=    -422.8591849     RMS=8.416758361     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   24.11     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 245 RMS= 0.0440 Dev= 0.72% S= 18.36 time= 12.82
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=  36.15

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1264 steps. Energy=    -450.5501243       time=      13.65
 Minus side of path:                    1243 steps. Energy=    -449.3924540       time=      13.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.5501243  1.4384         -449.1117243 0.28073         -449.3924540  21.361  18.043   4.061  53.686
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -450.5501243  1.4384        -449.1117243 0.28073        -449.3924540  21.361  18.043   4.061  53.686

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

 Elapsed time=                                77.44
 OPTIM> # of energy calls=                          2 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=              5618 time=          41.59 %= 53.7
 OPTIM> # of energy+gradient+Hessian calls=        51 time=          14.93 %= 19.3
