
 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 22:11:54
  [-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=    -453.3771851     RMS force=    0.8565771498E-06
 OPTIM> Final energy  =    -457.6916478     RMS force=    0.9784493248E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      64.92618007    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.20495E+06
 decide> The unconnected minima in the chain and their distances are:
     2       58.89     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=    12
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    669 fraction=    0.990000 images=     6 time=       1.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    694 steps, energy/image=    -417.4713174     RMS=.9681997426     images=   7
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   62.32     Attempts, images and iterations=     0    18   630
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 630 RMS= 0.0415 Dev= 4.72% S= 70.77 time= 85.77
 Following    2 images are candidates for TS:    5   14  
 Converged to TS (number of iterations):        117
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=  89.21

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1380 steps. Energy=    -453.3771851       time=      16.52
 Minus side of path:                    1335 steps. Energy=    -456.4373368       time=      15.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3771851 0.44003         -452.9371589  3.5002         -456.4373368  35.612  32.913   2.537  85.944
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    21   30 from     0.12754E-01 to     0.12794E-01 ref=     5.3801    
 checkperc> Increasing con cutoff atoms    26   30 from     0.18053E-02 to     0.19690E-02 ref=     3.4051    
 checkperc> Increasing con cutoff atoms    27   30 from     0.17250E-02 to     0.20793E-02 ref=     2.1610    
 checkperc> Increasing con cutoff atoms    29   33 from     0.11425E-02 to     0.12961E-02 ref=     2.4451    
 checkperc> Increasing con cutoff atoms    29   35 from     0.83669E-02 to     0.84011E-02 ref=     2.8603    
 checkperc> Increasing con cutoff atoms    30   35 from     0.91158E-02 to     0.91189E-02 ref=     3.9421    
 checkperc> Increasing con cutoff atoms    41   42 from     0.14928E-01 to     0.15166E-01 ref=     2.1381    
 checkperc> Increasing con cutoff atoms    44   45 from     0.25064E-03 to     0.25336E-03 ref=     1.0903    
 checkperc> Increasing con cutoff atoms    53   54 from     0.95540E-02 to     0.97052E-02 ref=     2.1207    
 checkperc> Increasing con cutoff atoms    54   56 from     0.47315E-02 to     0.47329E-02 ref=     1.5406    
 checkperc> Increasing con cutoff atoms    59   74 from     0.23400E-01 to     0.26874E-01 ref=     3.9183    
 checkperc> Increasing con cutoff atoms    77   78 from     0.14646E-01 to     0.17914E-01 ref=     2.1287    
 checkperc> Increasing con cutoff atoms   105  106 from     0.35752E-02 to     0.36561E-02 ref=     1.0128    
 checkperc> Increasing con cutoff atoms   134  135 from     0.30995E-02 to     0.31168E-02 ref=     1.0112    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1186 steps. Energy=    -457.6916478       time=      12.31
 Minus side of path:                    1218 steps. Energy=    -458.1746497       time=      13.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.6916478 0.45195         -457.2396957 0.93495         -458.1746497  34.960  33.258   2.744  79.443
        Known (#2)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    50   53 from     0.11977E-01 to     0.12143E-01 ref=     2.0114    
 checkperc> Increasing con cutoff atoms    50   54 from     0.25262E-01 to     0.25879E-01 ref=     2.4931    
 checkperc> Increasing con cutoff atoms    51   54 from     0.51394E-01 to     0.52757E-01 ref=     2.8632    
 checkperc> Increasing con cutoff atoms    52   57 from     0.97081E-01 to     0.99051E-01 ref=     2.7405    
 checkperc> Increasing con cutoff atoms    53   54 from     0.97052E-02 to     0.99335E-02 ref=     2.1207    
 checkperc> Increasing con cutoff atoms    55   59 from     0.14341     to     0.14442     ref=     2.8372    
 checkperc> Increasing con cutoff atoms    56   59 from     0.43680E-02 to     0.44220E-02 ref=     1.5027    
 checkperc> Increasing con cutoff atoms    56   64 from     0.13152E-01 to     0.13243E-01 ref=     3.8196    
 checkperc> Increasing con cutoff atoms    56   65 from     0.20306E-01 to     0.20430E-01 ref=     5.1109    
 checkperc> Increasing con cutoff atoms    56   66 from     0.13217E-01 to     0.13318E-01 ref=     5.9794    
 checkperc> Increasing con cutoff atoms    56   67 from     0.34516E-01 to     0.34686E-01 ref=     5.5184    
 checkperc> Increasing con cutoff atoms    56   68 from     0.35298E-01 to     0.35474E-01 ref=     6.5958    
 checkperc> Increasing con cutoff atoms    56   69 from     0.43741E-01 to     0.43928E-01 ref=     4.8223    
 checkperc> Increasing con cutoff atoms    56   70 from     0.48335E-01 to     0.48541E-01 ref=     5.5499    
 checkperc> Increasing con cutoff atoms    56   71 from     0.45925E-01 to     0.46097E-01 ref=     3.4328    
 checkperc> Increasing con cutoff atoms    56   73 from     0.23720E-01 to     0.23830E-01 ref=     2.6887    
 checkperc> Increasing con cutoff atoms    57   59 from     0.94830E-02 to     0.97152E-02 ref=     2.1159    
 checkperc> Increasing con cutoff atoms    59   65 from     0.45596E-02 to     0.45793E-02 ref=     3.6927    
 checkperc> Increasing con cutoff atoms    59   66 from     0.20527E-02 to     0.20598E-02 ref=     4.5052    
 checkperc> Increasing con cutoff atoms    59   67 from     0.84992E-02 to     0.85298E-02 ref=     4.2972    
 checkperc> Increasing con cutoff atoms    59   68 from     0.83090E-02 to     0.83414E-02 ref=     5.3775    
 checkperc> Increasing con cutoff atoms    60   62 from     0.14386E-02 to     0.14475E-02 ref=     1.3803    
 checkperc> Increasing con cutoff atoms    60   64 from     0.26300E-02 to     0.26588E-02 ref=     2.2808    
 checkperc> Increasing con cutoff atoms    60   65 from     0.38903E-02 to     0.39179E-02 ref=     3.6622    
 checkperc> Increasing con cutoff atoms    60   66 from     0.71061E-02 to     0.71467E-02 ref=     4.1932    
 checkperc> Increasing con cutoff atoms    61   65 from     0.53697E-02 to     0.54246E-02 ref=     4.6640    
 checkperc> Increasing con cutoff atoms    61   66 from     0.98442E-02 to     0.99311E-02 ref=     5.0783    
 checkperc> Increasing con cutoff atoms    62   64 from     0.13128E-02 to     0.13380E-02 ref=     1.3782    
 checkperc> Increasing con cutoff atoms    62   65 from     0.45912E-02 to     0.46274E-02 ref=     2.5497    
 checkperc> Increasing con cutoff atoms    62   67 from     0.33874E-02 to     0.34144E-02 ref=     3.7627    
 checkperc> Increasing con cutoff atoms    62   68 from     0.41838E-02 to     0.42138E-02 ref=     4.6863    
 checkperc> Increasing con cutoff atoms    62   69 from     0.29507E-02 to     0.29662E-02 ref=     4.1392    
 checkperc> Increasing con cutoff atoms    62   70 from     0.29806E-02 to     0.29895E-02 ref=     5.2188    
 checkperc> Increasing con cutoff atoms    64   74 from     0.51300E-01 to     0.54032E-01 ref=     6.0810    
 checkperc> Increasing con cutoff atoms    65   73 from     0.38614E-02 to     0.38949E-02 ref=     2.4846    
 checkperc> Increasing con cutoff atoms    66   73 from     0.29788E-02 to     0.30101E-02 ref=     3.4582    
 checkperc> Increasing con cutoff atoms    66   74 from     0.64280E-01 to     0.67260E-01 ref=     8.1890    
 checkperc> Increasing con cutoff atoms    67   73 from     0.56291E-02 to     0.56647E-02 ref=     2.8584    
 checkperc> Increasing con cutoff atoms    68   73 from     0.55643E-02 to     0.56013E-02 ref=     3.9410    
 checkperc> Increasing con cutoff atoms   114  134 from     0.21164E-01 to     0.22901E-01 ref=     2.4615    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     5040.8    
 decide> The unconnected minima in the chain and their distances are:
     4       17.13     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=   159
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     65 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     90 steps, energy/image=    -391.1191506     RMS=19.68100146     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   22.25     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.7388 Dev= 0.45% S= 17.94 time= 9.43
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  28.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1345 steps. Energy=    -458.1746497       time=      15.61
 Minus side of path:                    1194 steps. Energy=    -456.4373368       time=      13.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.1746497  2.7564         -455.4182021  1.0191         -456.4373368  25.536  17.131   8.126  26.828
        Known (#4)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -453.3771851 0.44003        -452.9371589  3.5002        -456.4373368  35.612  32.913   2.537  85.944
   3     -456.4373368  1.0191        -455.4182021  2.7564        -458.1746497  25.536  17.131   8.126  26.828
   2     -458.1746497 0.93495        -457.2396957 0.45195        -457.6916478  34.960  33.258   2.744  79.443

 Number of TS in the path       =      3
 Number of cycles               =      2

 Elapsed time=                               303.90
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             24228 time=         179.76 %= 59.2
 OPTIM> # of energy+gradient+Hessian calls=       178 time=          52.79 %= 17.4
