
 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 17:41:49
  [-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=    -452.8246175     RMS force=    0.9928870956E-06
 OPTIM> Final energy  =    -447.5232955     RMS force=    0.9781509881E-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      123.2614650    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.10707E+07
 decide> The unconnected minima in the chain and their distances are:
     2      102.18     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=     0
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1823 fraction=    0.990000 images=    12 time=       3.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1848 steps, energy/image=    -373.9086282     RMS=.9386997173     images=  13
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   106.9     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.6569044378E-01
 Double-ended search iterations= 805 RMS= 0.0319 Dev= 4.54% S= 119.18 time= 139.04
 Following    2 images are candidates for TS:    9   18  
 Converged to TS (number of iterations):        186
 Converged to TS (number of iterations):         73
 DNEB run yielded 2 true transition state(s) time= 144.41

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1367 steps. Energy=    -446.3106749       time=      14.99
 Minus side of path:                    1792 steps. Energy=    -447.8607302       time=      23.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.3106749 0.30651         -446.0041678  1.8566         -447.8607302  55.849  47.892   1.838 118.588
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    29   34 from     0.12218E-02 to     0.12360E-02 ref=     3.4184    
 checkperc> Increasing con cutoff atoms   105  106 from     0.45032E-02 to     0.52936E-02 ref=     1.0142    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1778 steps. Energy=    -447.5232955       time=      24.93
 Minus side of path:                    1464 steps. Energy=    -447.7433070       time=      19.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5232955 0.67404         -446.8492571 0.89405         -447.7433070  55.339  45.182   1.482 147.072
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    84   85 from     0.42890E-02 to     0.43025E-02 ref=     1.7692    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     89048.    
 decide> The unconnected minima in the chain and their distances are:
     5       27.37     3     4       40.87     1 
 

 tryconnect> Interpolation for minima 3_U 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=    70
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    150 fraction=    0.990000 images=     3 time=       0.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    175 steps, energy/image=    -391.1140058     RMS=7.264412302     images=   4
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   35.77     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant      1.059966752    
 Double-ended search iterations= 350 RMS= 0.0336 Dev= 0.50% S= 28.75 time= 26.48
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  49.80

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1428 steps. Energy=    -447.7433070       time=      15.30
 Minus side of path:                    1962 steps. Energy=    -447.8607302       time=      24.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7433070  2.4772         -445.2661334  2.5946         -447.8607302  53.780  37.951   2.257  96.577
        Known (#5)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 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=    40
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    282 fraction=    0.990000 images=     5 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    307 steps, energy/image=    -435.8207077     RMS=1.008481357     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   42.00     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0413 Dev= 1.03% S= 42.99 time= 37.67
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=  53.88

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1291 steps. Energy=    -448.3890306       time=      16.87
 Minus side of path:                    1204 steps. Energy=    -447.8607302       time=      14.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3890306 0.53141         -447.8576188 0.31115E-02     -447.8607302  19.035  18.883   2.049 106.410
        *NEW* (Placed in 6)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    65   71 from     0.20565E-02 to     0.20828E-02 ref=     2.8201    
 checkperc> Increasing con cutoff atoms    65   72 from     0.30391E-02 to     0.33019E-02 ref=     3.8996    
 checkperc> Increasing con cutoff atoms    66   71 from     0.20999E-02 to     0.21433E-02 ref=     3.9012    
 checkperc> Increasing con cutoff atoms    66   72 from     0.30720E-02 to     0.33464E-02 ref=     4.9808    
 checkperc> Increasing con cutoff atoms    67   70 from     0.96503E-03 to     0.10041E-02 ref=     2.1582    
 checkperc> Increasing con cutoff atoms    67   71 from     0.81213E-03 to     0.10924E-02 ref=     2.4443    
 checkperc> Increasing con cutoff atoms    67   72 from     0.39906E-02 to     0.40055E-02 ref=     3.4156    
 checkperc> Increasing con cutoff atoms    68   70 from     0.10493E-02 to     0.18324E-02 ref=     2.4853    
 checkperc> Increasing con cutoff atoms    69   70 from     0.32514E-03 to     0.33556E-03 ref=     1.0822    
 checkperc> Increasing con cutoff atoms    78   83 from     0.24778E-01 to     0.25097E-01 ref=     2.5735    
 checkperc> Increasing con cutoff atoms    79   83 from     0.79278E-01 to     0.81452E-01 ref=     2.7519    
 checkperc> Increasing con cutoff atoms   105  106 from     0.52936E-02 to     0.55954E-02 ref=     1.0142    
 checkperc> Increasing con cutoff atoms   144  148 from     0.13175E-01 to     0.14136E-01 ref=     2.8838    
 checkperc> Increasing con cutoff atoms   146  148 from     0.41210E-02 to     0.45003E-02 ref=     2.1576    
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     24497.    
 decide> The unconnected minima in the chain and their distances are:
     6       29.01     1 
 

 tryconnect> Interpolation for minima 1_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=    67
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    153 fraction=    0.990000 images=     3 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    178 steps, energy/image=    -401.3199106     RMS=11.54522936     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   32.95     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0433 Dev= 2.07% S= 30.87 time= 21.70
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=  36.27

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1429 steps. Energy=    -452.4924236       time=      16.60
 Minus side of path:                    1253 steps. Energy=    -448.3890306       time=      13.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4924236  4.1656         -448.3267768 0.62254E-01     -448.3890306  33.957  29.992   2.505  87.015
        *NEW* (Placed in 7)                                     Known (#6)
 checkperc> Increasing con cutoff atoms    69   71 from     0.22069E-03 to     0.24792E-03 ref=     1.4087    
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     15.791    
 decide> The unconnected minima in the chain and their distances are:
     7        2.51     1 
 

 tryconnect> Interpolation for minima 1_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=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     19 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     44 steps, energy/image=    -448.1496896     RMS=.4163865749     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      1     7 dist=   10.98     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 1.6308 Dev= 6.78% S= 23.66 time= 2.39
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 131.22
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     31.582    
 decide> The unconnected minima in the chain and their distances are:
     7        2.51     1 
 

 tryconnect> Interpolation for minima 1_S and 7_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     18 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     43 steps, energy/image=    -448.2711278     RMS=.1103774013     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      1     7 dist=   3.358     Attempts, images and iterations=     1     7   245
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 245 RMS= 0.0189 Dev= 1.88% S= 3.06 time= 12.92
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=  19.04

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1195 steps. Energy=    -452.4924236       time=      14.16
 Minus side of path:                    1150 steps. Energy=    -452.8246175       time=      12.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4924236 0.60533         -451.8870959 0.93752         -452.8246175   2.758   2.506  31.844   6.846
        Known (#7)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -452.8246175 0.93752        -451.8870959 0.60533        -452.4924236   2.758   2.506  31.844   6.846
   5     -452.4924236  4.1656        -448.3267768 0.62254E-01    -448.3890306  33.957  29.992   2.505  87.015
   4     -448.3890306 0.53141        -447.8576188 0.31115E-02    -447.8607302  19.035  18.883   2.049 106.410
   3     -447.8607302  2.5946        -445.2661334  2.4772        -447.7433070  53.780  37.951   2.257  96.577
   2     -447.7433070 0.89405        -446.8492571 0.67404        -447.5232955  55.339  45.182   1.482 147.072

 Number of TS in the path       =      5
 Number of cycles               =      5

 Elapsed time=                               899.64
 OPTIM> # of energy calls=                         12 time=           0.09 %=  0.0
 OPTIM> # of energy+gradient calls=             60609 time=         450.55 %= 50.1
 OPTIM> # of energy+gradient+Hessian calls=       739 time=         213.39 %= 23.7
