
 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 17:42:28
  [-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=    -447.7272639     RMS force=    0.9962555345E-06
 OPTIM> Final energy  =    -446.9783807     RMS force=    0.9706039600E-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      69.11730627    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.13924E+06
 decide> The unconnected minima in the chain and their distances are:
     2       51.76     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=    50
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    775 fraction=    0.990000 images=     6 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    800 steps, energy/image=     339.7190119     RMS=16.54327774     images=   7
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   55.02     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 560 RMS= 0.0471 Dev= 4.25% S= 66.77 time= 68.55
 Following    2 images are candidates for TS:    5   12  
 Converged to TS (number of iterations):         35
 Converged to TS (number of iterations):        159
 DNEB run yielded 2 true transition state(s) time= 119.24

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1363 steps. Energy=    -447.7272639       time=      17.91
 Minus side of path:                    1962 steps. Energy=    -454.1323608       time=      31.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7272639  1.4654         -446.2619066  7.8705         -454.1323608  61.051  52.455   7.029  31.016
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   212  214 from     0.62961E-02 to     0.63298E-02 ref=     1.0176    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1336 steps. Energy=    -449.4230214       time=      14.82
 Minus side of path:                    1323 steps. Energy=    -449.2842051       time=      14.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4230214  2.4768         -446.9461932  2.3380         -449.2842051  30.656  13.452   3.169  68.785
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    95   97 from     0.13673E-02 to     0.14499E-02 ref=     1.0903    
 checkperc> Increasing con cutoff atoms   148  149 from     0.46527E-02 to     0.65304E-02 ref=     2.1644    
 checkperc> Increasing con cutoff atoms   148  150 from     0.12207E-01 to     0.13167E-01 ref=     2.4985    
 checkperc> Increasing con cutoff atoms   148  151 from     0.56043E-02 to     0.66895E-02 ref=     3.4132    
 checkperc> Increasing con cutoff atoms   148  152 from     0.59323E-02 to     0.71354E-02 ref=     4.3092    
 checkperc> Increasing con cutoff atoms   150  151 from     0.64561E-02 to     0.68932E-02 ref=     2.1640    
 checkperc> Increasing con cutoff atoms   198  203 from     0.51259E-01 to     0.52648E-01 ref=     2.5995    
 checkperc> Increasing con cutoff atoms   213  215 from     0.10614E-01 to     0.16419E-01 ref=     1.6400    
 checkperc> Increasing con cutoff atoms    78   82 from     0.13354E-01 to     0.14557E-01 ref=     2.1518    
 checkperc> Increasing con cutoff atoms    80   82 from     0.19746E-02 to     0.27407E-02 ref=     1.0891    
 checkperc> Increasing con cutoff atoms    82   83 from     0.14175E-01 to     0.18078E-01 ref=     2.1403    
 checkperc> Increasing con cutoff atoms    82   85 from     0.12967E-01 to     0.15202E-01 ref=     3.0397    
 checkperc> Increasing con cutoff atoms   114  136 from     0.31901E-01 to     0.35341E-01 ref=     3.8662    
 checkperc> Increasing con cutoff atoms   114  137 from     0.10895     to     0.11710     ref=     4.1884    
 checkperc> Increasing con cutoff atoms   136  160 from     0.33340E-01 to     0.39110E-01 ref=     3.8890    
 checkperc> Increasing con cutoff atoms   141  151 from     0.18391E-01 to     0.18970E-01 ref=     3.8988    
 checkperc> Increasing con cutoff atoms   141  152 from     0.18198E-01 to     0.25659E-01 ref=     4.8092    
 checkperc> Increasing con cutoff atoms   142  151 from     0.50498E-02 to     0.58796E-02 ref=     4.6352    
 checkperc> Increasing con cutoff atoms   142  152 from     0.58244E-02 to     0.10402E-01 ref=     5.6555    
 checkperc> Increasing con cutoff atoms   143  152 from     0.64814E-02 to     0.11481E-01 ref=     6.7266    
 checkperc> Increasing con cutoff atoms   147  148 from     0.17060E-02 to     0.18137E-02 ref=     1.0800    
 checkperc> Increasing con cutoff atoms   147  152 from     0.52666E-02 to     0.58306E-02 ref=     3.4086    
 checkperc> Increasing con cutoff atoms   148  152 from     0.71354E-02 to     0.75820E-02 ref=     4.3092    
 checkperc> Increasing con cutoff atoms   149  152 from     0.48379E-02 to     0.55729E-02 ref=     2.1598    
 checkperc> Increasing con cutoff atoms   151  153 from     0.93834E-03 to     0.13669E-02 ref=     1.4083    
 checkperc> Increasing con cutoff atoms   151  155 from     0.74604E-02 to     0.86902E-02 ref=     2.4630    
 checkperc> Increasing con cutoff atoms   152  153 from     0.38178E-02 to     0.79038E-02 ref=     2.1586    
 checkperc> Increasing con cutoff atoms   152  155 from     0.67612E-02 to     0.11035E-01 ref=     3.4344    
 checkperc> Increasing con cutoff atoms   153  155 from     0.29195E-02 to     0.36070E-02 ref=     1.4147    
 checkperc> Increasing con cutoff atoms   206  210 from     0.96008E-02 to     0.97876E-02 ref=     2.1516    
 checkperc> Increasing con cutoff atoms   209  214 from     0.64916E-02 to     0.14992E-01 ref=     2.0836    
 checkperc> Increasing con cutoff atoms   210  214 from     0.51179E-01 to     0.65331E-01 ref=     2.4089    
 checkperc> Increasing con cutoff atoms   211  215 from     0.72193E-02 to     0.89045E-02 ref=     2.9807    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3553.9    
 decide> The unconnected minima in the chain and their distances are:
     2       15.24     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S 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=   188
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     58 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     83 steps, energy/image=    -351.1267720     RMS=22.81231090     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   22.22     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 210 RMS= 0.2158 Dev= 1.87% S= 17.05 time= 9.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  35.56

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1402 steps. Energy=    -452.6624608       time=      16.08
 Minus side of path:                    1250 steps. Energy=    -446.9783807       time=      13.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.6624608  5.6898         -446.9726148 0.57659E-02     -446.9783807  18.151  17.607   4.372  49.864
        *NEW* (Placed in 6)                                     Known (#2)
 checkperc> Increasing con cutoff atoms   209  212 from     0.29770E-02 to     0.32091E-02 ref=     1.4895    
 checkperc> Increasing con cutoff atoms   209  213 from     0.11992E-01 to     0.12065E-01 ref=     2.0921    
 checkperc> Increasing con cutoff atoms   210  213 from     0.11278E-01 to     0.15241E-01 ref=     2.9763    
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     3598.3    
 decide> The unconnected minima in the chain and their distances are:
     6       15.31     3 
 

 tryconnect> Interpolation for minima 3_S and 6_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=   154
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     92 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    117 steps, energy/image=    -440.6897383     RMS=7.094488974     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      3     6 dist=   21.74     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 210 RMS= 0.0809 Dev= 1.28% S= 15.74 time= 9.56
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=  24.46

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1285 steps. Energy=    -454.1373042       time=      14.32
 Minus side of path:                    1271 steps. Energy=    -452.6624608       time=      13.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.1373042  3.6591         -450.4781817  2.1843         -452.6624608   9.246   8.722  13.574  16.061
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     709.51    
 decide> The unconnected minima in the chain and their distances are:
     7        8.91     3 
 

 tryconnect> Interpolation for minima 3_S and 7_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=   197
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     23 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     48 steps, energy/image=    -449.2609326     RMS=.3372174442     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   15.14     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 0.0228 Dev= 0.34% S= 8.95 time= 4.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  25.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1287 steps. Energy=    -454.1323608       time=      13.79
 Minus side of path:                    1287 steps. Energy=    -454.1373042       time=      13.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.1323608 0.54097E-01     -454.0782639 0.59040E-01     -454.1373042   9.135   8.910   3.335  65.360
        Known (#3)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -447.7272639  1.4654        -446.2619066  7.8705        -454.1323608  61.051  52.455   7.029  31.016
   5     -454.1323608 0.54097E-01    -454.0782639 0.59040E-01    -454.1373042   9.135   8.910   3.335  65.360
   4     -454.1373042  3.6591        -450.4781817  2.1843        -452.6624608   9.246   8.722  13.574  16.061
   3     -452.6624608  5.6898        -446.9726148 0.57659E-02    -446.9783807  18.151  17.607   4.372  49.864

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

 Elapsed time=                               467.07
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             32854 time=         247.08 %= 52.9
 OPTIM> # of energy+gradient+Hessian calls=       295 time=          87.53 %= 18.7
