
 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 22:14:30
  [-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=    -457.0984179     RMS force=    0.9582458728E-06
 OPTIM> Final energy  =    -456.0341414     RMS force=    0.9509654834E-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    18   26 from     0.50240E-02 to     0.50448E-02 ref=     3.8121    
 checkperc> Increasing con cutoff atoms    18   28 from     0.70737E-02 to     0.83989E-02 ref=     5.9699    
 checkperc> Increasing con cutoff atoms    21   26 from     0.19268E-02 to     0.20415E-02 ref=     2.3468    
 checkperc> Increasing con cutoff atoms    21   28 from     0.44848E-02 to     0.62865E-02 ref=     4.5017    
 checkperc> Increasing con cutoff atoms    22   35 from     0.12006E-02 to     0.16029E-02 ref=     2.2454    
 checkperc> Increasing con cutoff atoms    23   24 from     0.23695E-02 to     0.27580E-02 ref=     2.1928    
 checkperc> Increasing con cutoff atoms    23   25 from     0.68780E-02 to     0.69650E-02 ref=     2.5636    
 checkperc> Increasing con cutoff atoms    24   25 from     0.55957E-02 to     0.58043E-02 ref=     1.0185    
 checkperc> Increasing con cutoff atoms    25   26 from     0.67281E-02 to     0.86862E-02 ref=     2.1348    
 checkperc> Increasing con cutoff atoms    25   27 from     0.93044E-02 to     0.12872E-01 ref=     2.9313    
 checkperc> Increasing con cutoff atoms    25   28 from     0.12529E-01 to     0.16515E-01 ref=     2.8914    
 checkperc> Increasing con cutoff atoms    25   29 from     0.88902E-02 to     0.11552E-01 ref=     4.2910    
 checkperc> Increasing con cutoff atoms    25   30 from     0.95609E-02 to     0.11721E-01 ref=     5.0812    
 checkperc> Increasing con cutoff atoms    25   31 from     0.72587E-02 to     0.97207E-02 ref=     4.9072    
 checkperc> Increasing con cutoff atoms    25   32 from     0.86224E-02 to     0.10877E-01 ref=     5.9860    
 checkperc> Increasing con cutoff atoms    25   33 from     0.58754E-02 to     0.71287E-02 ref=     4.4778    
 checkperc> Increasing con cutoff atoms    25   34 from     0.60206E-02 to     0.72469E-02 ref=     5.3614    
 checkperc> Increasing con cutoff atoms    25   35 from     0.60053E-02 to     0.70122E-02 ref=     3.2083    
 checkperc> Increasing con cutoff atoms    26   27 from     0.81021E-03 to     0.11053E-02 ref=     1.4030    
 checkperc> Increasing con cutoff atoms    26   29 from     0.12154E-02 to     0.13084E-02 ref=     2.4216    
 checkperc> Increasing con cutoff atoms    26   35 from     0.78530E-03 to     0.94830E-03 ref=     1.4283    
 checkperc> Increasing con cutoff atoms    27   29 from     0.53012E-03 to     0.58216E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    28   29 from     0.27516E-02 to     0.31258E-02 ref=     2.1631    
 checkperc> Increasing con cutoff atoms    28   30 from     0.38496E-02 to     0.41211E-02 ref=     2.4960    
 checkperc> Increasing con cutoff atoms    28   31 from     0.25380E-02 to     0.29428E-02 ref=     3.4147    
 checkperc> Increasing con cutoff atoms    28   32 from     0.33087E-02 to     0.37792E-02 ref=     4.3086    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.13381E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    29   34 from     0.14292E-02 to     0.20405E-02 ref=     3.4183    
 checkperc> Increasing con cutoff atoms    30   34 from     0.21544E-02 to     0.27885E-02 ref=     4.3093    
 checkperc> Increasing con cutoff atoms    31   34 from     0.17415E-02 to     0.18765E-02 ref=     2.1569    
 checkperc> Increasing con cutoff atoms    36   38 from     0.23735E-02 to     0.25414E-02 ref=     1.3421    
 checkperc> Increasing con cutoff atoms    38   40 from     0.54683E-02 to     0.54709E-02 ref=     1.4766    
 checkperc> Increasing con cutoff atoms    39   40 from     0.13770E-01 to     0.14394E-01 ref=     2.1373    
 checkperc> Increasing con cutoff atoms    41   44 from     0.65831E-01 to     0.68516E-01 ref=     2.6830    
 checkperc> Increasing con cutoff atoms    42   47 from     0.41133E-02 to     0.42217E-02 ref=     2.1681    
 checkperc> Increasing con cutoff atoms    44   48 from     0.16213E-01 to     0.16283E-01 ref=     2.3802    
 checkperc> Increasing con cutoff atoms    45   47 from     0.23345E-02 to     0.26303E-02 ref=     1.7767    
 checkperc> Increasing con cutoff atoms    84   87 from     0.10885     to     0.13563     ref=     3.1839    
 checkperc> Increasing con cutoff atoms    84   88 from     0.14005     to     0.14270     ref=     2.6522    
 checkperc> Increasing con cutoff atoms    87   88 from     0.11823E-01 to     0.12844E-01 ref=     2.1879    
 checkperc> Increasing con cutoff atoms    93   94 from     0.17933E-02 to     0.21622E-02 ref=     1.0899    
 checkperc> Increasing con cutoff atoms   122  130 from     0.80215E-01 to     0.84330E-01 ref=     2.7730    
 checkperc> Increasing con cutoff atoms   126  129 from     0.63996E-01 to     0.66665E-01 ref=     2.4249    
 checkperc> Increasing con cutoff atoms   162  163 from     0.82638E-03 to     0.86092E-03 ref=     1.0926    
 checkperc> Increasing con cutoff atoms   179  189 from     0.11936E-01 to     0.12097E-01 ref=     3.8945    
 checkperc> Increasing con cutoff atoms   179  190 from     0.12082E-01 to     0.12674E-01 ref=     4.8042    
 checkperc> Increasing con cutoff atoms   180  182 from     0.19499E-02 to     0.21204E-02 ref=     1.3801    
 checkperc> Increasing con cutoff atoms   180  186 from     0.10377E-01 to     0.10707E-01 ref=     4.1922    
 checkperc> Increasing con cutoff atoms   180  188 from     0.35120E-02 to     0.38167E-02 ref=     5.6712    
 checkperc> Increasing con cutoff atoms   182  188 from     0.70369E-02 to     0.73169E-02 ref=     4.6852    
 checkperc> Increasing con cutoff atoms   189  191 from     0.79797E-03 to     0.10528E-02 ref=     1.4086    
 checkperc> Increasing con cutoff atoms   189  193 from     0.48914E-02 to     0.50659E-02 ref=     2.4611    
 checkperc> Increasing con cutoff atoms   190  191 from     0.27902E-02 to     0.29140E-02 ref=     2.1607    
 checkperc> Increasing con cutoff atoms   190  193 from     0.38256E-02 to     0.39746E-02 ref=     3.4333    
 initialise> Interpolation metric value for minima 1 and 2 is      19.04795932    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     5827.7    
 decide> The unconnected minima in the chain and their distances are:
     2       17.98     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=   158
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -448.1440596     RMS=.4344981259     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   22.95     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 210 RMS= 0.2883 Dev= 1.19% S= 18.86 time= 9.52
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  28.78

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1235 steps. Energy=    -457.7255429       time=      16.08
 Minus side of path:                    1258 steps. Energy=    -456.0341414       time=      15.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.7255429  4.9442         -452.7813580  3.2528         -456.0341414  12.525  10.828  14.061  15.504
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    21   25 from     0.74080E-02 to     0.80422E-02 ref=     3.1995    
 checkperc> Increasing con cutoff atoms    22   25 from     0.59001E-02 to     0.62458E-02 ref=     2.1146    
 checkperc> Increasing con cutoff atoms    22   26 from     0.16039E-02 to     0.16881E-02 ref=     2.2826    
 checkperc> Increasing con cutoff atoms    22   27 from     0.20176E-02 to     0.21758E-02 ref=     3.6652    
 checkperc> Increasing con cutoff atoms    24   25 from     0.58043E-02 to     0.59644E-02 ref=     1.0185    
 checkperc> Increasing con cutoff atoms    40   48 from     0.26768E-01 to     0.27236E-01 ref=     2.4207    
 checkperc> Increasing con cutoff atoms    44   46 from     0.19209E-03 to     0.19779E-03 ref=     1.0904    
 checkperc> Increasing con cutoff atoms    44   48 from     0.16283E-01 to     0.16345E-01 ref=     2.3802    
 checkperc> Increasing con cutoff atoms    78   84 from     0.13426     to     0.15063     ref=     2.8348    
 checkperc> Increasing con cutoff atoms    81   85 from     0.11597     to     0.12987     ref=     2.4580    
 checkperc> Increasing con cutoff atoms    82   86 from     0.13016     to     0.16446     ref=     2.7409    
 checkperc> Increasing con cutoff atoms    82   89 from     0.12266     to     0.12760     ref=     2.6624    
 checkperc> Increasing con cutoff atoms    84   87 from     0.13563     to     0.14398     ref=     3.1839    
 checkperc> Increasing con cutoff atoms    84   88 from     0.14270     to     0.15599     ref=     2.6522    
 checkperc> Increasing con cutoff atoms   141  144 from     0.42522E-02 to     0.44467E-02 ref=     2.2370    
 checkperc> Increasing con cutoff atoms   184  192 from     0.53922E-02 to     0.57163E-02 ref=     3.4034    
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     5033.1    
 decide> The unconnected minima in the chain and their distances are:
     3       17.12     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=   160
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     59 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     84 steps, energy/image=    -450.0938690     RMS=.4815687630     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   23.63     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 245 RMS= 0.0171 Dev= 1.06% S= 17.21 time= 12.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=  39.19

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1183 steps. Energy=    -457.0984179       time=      12.50
 Minus side of path:                    1271 steps. Energy=    -457.7255429       time=      14.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.0984179 0.21881E-01     -457.0765371 0.64901         -457.7255429  18.610  17.133   3.638  59.925
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -457.0984179 0.21881E-01    -457.0765371 0.64901        -457.7255429  18.610  17.133   3.638  59.925
   1     -457.7255429  4.9442        -452.7813580  3.2528        -456.0341414  12.525  10.828  14.061  15.504

 Number of TS in the path       =      2
 Number of cycles               =      2

 Elapsed time=                               150.65
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             10621 time=          78.90 %= 52.4
 OPTIM> # of energy+gradient+Hessian calls=        93 time=          26.83 %= 17.8
