
 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 17:42:19
  [-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:         0.05000       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=    -458.3319363     RMS force=    0.9703682089E-06
 OPTIM> Final energy  =    -454.6973722     RMS force=    0.7868347480E-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      38.25518669    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     43645.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.17     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=    42
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    295 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    320 steps, energy/image=    -442.0285491     RMS=.4538875617     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   43.24     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1677 Dev= 3.81% S= 41.65 time= 38.41
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=  51.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1304 steps. Energy=    -454.6973722       time=      15.13
 Minus side of path:                    1258 steps. Energy=    -454.5098898       time=      14.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.6973722  2.6833         -452.0140422  2.4958         -454.5098898  13.824  10.759  16.565  13.161
        Known (#2)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    40   58 from     0.13015     to     0.13016     ref=     5.7047    
 checkperc> Increasing con cutoff atoms    54   58 from     0.90080E-02 to     0.90094E-02 ref=     2.1528    
 checkperc> Increasing con cutoff atoms    55   74 from     0.14083E-01 to     0.14086E-01 ref=     2.1463    
 checkperc> Increasing con cutoff atoms    55   75 from     0.12085     to     0.12087     ref=     3.1545    
 checkperc> Increasing con cutoff atoms    56   74 from     0.24877E-01 to     0.24885E-01 ref=     2.5460    
 checkperc> Increasing con cutoff atoms    59   74 from     0.43412E-01 to     0.43420E-01 ref=     3.8957    
 checkperc> Increasing con cutoff atoms    93   94 from     0.13251E-02 to     0.13305E-02 ref=     1.0904    
 checkperc> Increasing con cutoff atoms   114  119 from     0.49869E-01 to     0.49935E-01 ref=     2.5994    
 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=     42832.    
 decide> The unconnected minima in the chain and their distances are:
     3       34.95     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=    41
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    334 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    359 steps, energy/image=    -430.4990931     RMS=1.168614447     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   43.16     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.4855829818    
 Double-ended search iterations= 420 RMS= 0.0489 Dev= 1.58% S= 36.71 time= 38.56
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=  60.82

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1285 steps. Energy=    -454.5098899       time=      15.82
 Minus side of path:                    1568 steps. Energy=    -458.1809981       time=      18.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.5098899 0.35839         -454.1514950  4.0295         -458.1809981  52.549  46.366   1.743 125.043
        Known (#3)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    19   21 from     0.16564E-01 to     0.16775E-01 ref=     2.1142    
 checkperc> Increasing con cutoff atoms    31   35 from     0.15432E-02 to     0.16203E-02 ref=     2.4575    
 checkperc> Increasing con cutoff atoms    45   47 from     0.21364E-02 to     0.21522E-02 ref=     1.7770    
 checkperc> Increasing con cutoff atoms    54   74 from     0.39319E-02 to     0.39755E-02 ref=     1.5425    
 checkperc> Increasing con cutoff atoms    55   75 from     0.12087     to     0.12759     ref=     3.1545    
 checkperc> Increasing con cutoff atoms    55   78 from     0.12441     to     0.12994     ref=     4.0623    
 checkperc> Increasing con cutoff atoms    56   74 from     0.24885E-01 to     0.25903E-01 ref=     2.5460    
 checkperc> Increasing con cutoff atoms    57   67 from     0.82048E-01 to     0.82238E-01 ref=     6.2890    
 checkperc> Increasing con cutoff atoms    57   68 from     0.86185E-01 to     0.86375E-01 ref=     7.3675    
 checkperc> Increasing con cutoff atoms    57   69 from     0.11477     to     0.11490     ref=     5.6790    
 checkperc> Increasing con cutoff atoms    57   70 from     0.13603     to     0.13611     ref=     6.4347    
 checkperc> Increasing con cutoff atoms    57   71 from     0.11569     to     0.11580     ref=     4.3134    
 checkperc> Increasing con cutoff atoms    57   73 from     0.59435E-01 to     0.59616E-01 ref=     3.4566    
 checkperc> Increasing con cutoff atoms    58   74 from     0.14472     to     0.14893     ref=     2.7109    
 checkperc> Increasing con cutoff atoms    80   81 from     0.27178E-02 to     0.27376E-02 ref=     1.0884    
 checkperc> Increasing con cutoff atoms    93   96 from     0.12373E-01 to     0.13069E-01 ref=     2.1614    
 checkperc> Increasing con cutoff atoms   105  108 from     0.13593E-01 to     0.14165E-01 ref=     2.0995    
 checkperc> Increasing con cutoff atoms   128  130 from     0.52806E-02 to     0.52941E-02 ref=     1.0164    
 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=     63550.    
 decide> The unconnected minima in the chain and their distances are:
     4       39.87     1 
 

 tryconnect> Interpolation for minima 1_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=    21
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    387 fraction=    0.990000 images=     4 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    412 steps, energy/image=    -449.0400672     RMS=.6957477965     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   43.81     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0316 Dev= 1.80% S= 42.65 time= 44.17
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=  44.12

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1268 steps. Energy=    -458.1809981       time=      12.89
 Minus side of path:                    1426 steps. Energy=    -457.8258844       time=      15.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.1809981 0.55309         -457.6279078 0.19798         -457.8258844  23.842  18.594   7.408  29.427
        Known (#4)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    31   35 from     0.16203E-02 to     0.16593E-02 ref=     2.4575    
 checkperc> Increasing con cutoff atoms    54   74 from     0.39755E-02 to     0.39830E-02 ref=     1.5425    
 checkperc> Increasing con cutoff atoms    55   75 from     0.12759     to     0.12812     ref=     3.1545    
 checkperc> Increasing con cutoff atoms    55   78 from     0.12994     to     0.13044     ref=     4.0623    
 checkperc> Increasing con cutoff atoms    56   74 from     0.25903E-01 to     0.26014E-01 ref=     2.5460    
 checkperc> Increasing con cutoff atoms    57   67 from     0.82238E-01 to     0.82252E-01 ref=     6.2890    
 checkperc> Increasing con cutoff atoms    57   68 from     0.86375E-01 to     0.86390E-01 ref=     7.3675    
 checkperc> Increasing con cutoff atoms    57   69 from     0.11490     to     0.11492     ref=     5.6790    
 checkperc> Increasing con cutoff atoms    57   70 from     0.13611     to     0.13613     ref=     6.4347    
 checkperc> Increasing con cutoff atoms    57   71 from     0.11580     to     0.11582     ref=     4.3134    
 checkperc> Increasing con cutoff atoms    57   73 from     0.59616E-01 to     0.59629E-01 ref=     3.4566    
 checkperc> Increasing con cutoff atoms    58   74 from     0.14893     to     0.14928     ref=     2.7109    
 checkperc> Increasing con cutoff atoms    80   81 from     0.27376E-02 to     0.27393E-02 ref=     1.0884    
 checkperc> Increasing con cutoff atoms   105  108 from     0.14165E-01 to     0.14248E-01 ref=     2.0995    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     28974.    
 decide> The unconnected minima in the chain and their distances are:
     5       30.68     1 
 

 tryconnect> Interpolation for minima 1_S and 5_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=    40
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    179 fraction=    0.990000 images=     3 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    204 steps, energy/image=    -448.2282806     RMS=.5485637618     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   33.53     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0168 Dev= 1.14% S= 31.81 time= 26.17
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=  50.85

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1377 steps. Energy=    -458.3319363       time=      14.57
 Minus side of path:                    1277 steps. Energy=    -457.8258844       time=      13.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.3319363  1.1186         -457.2133149 0.61257         -457.8258844  34.181  30.702   2.035 107.137
        Known (#1)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -458.3319363  1.1186        -457.2133149 0.61257        -457.8258844  34.181  30.702   2.035 107.137
   3     -457.8258844 0.19798        -457.6279078 0.55309        -458.1809981  23.842  18.594   7.408  29.427
   2     -458.1809981  4.0295        -454.1514950 0.35839        -454.5098898  52.549  46.366   1.743 125.043
   1     -454.5098898  2.4958        -452.0140422  2.6833        -454.6973722  13.824  10.759  16.565  13.161

 Number of TS in the path       =      4
 Number of cycles               =      4

 Elapsed time=                               481.88
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             36085 time=         269.62 %= 56.0
 OPTIM> # of energy+gradient+Hessian calls=       340 time=          98.47 %= 20.4
