
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/27/2012 at 22:14:03
  [-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=    -451.4537995     RMS force=    0.9183379396E-06
 OPTIM> Final energy  =    -450.4708986     RMS force=    0.9670578179E-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      809.5762615    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.46433E+06
 decide> The unconnected minima in the chain and their distances are:
     2       76.63     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   1768 fraction=    0.990000 images=    10 time=       4.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1793 steps, energy/image=    -312.1166857     RMS=1.796041080     images=  11
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   93.17     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.7242371427E-01
 Double-ended search iterations= 805 RMS= 0.0296 Dev= 4.26% S= 117.35 time= 138.03
 Following    3 images are candidates for TS:    5   12   14  
 Converged to TS (number of iterations):         61
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        114
 Converged to TS (number of iterations):        124
 DNEB run yielded 3 true transition state(s) time= 172.38

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1571 steps. Energy=    -451.4537995       time=      17.48
 Minus side of path:                    1294 steps. Energy=    -451.5852727       time=      13.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4537995  2.3395         -449.1143342  2.4709         -451.5852727  39.807  31.812   3.632  60.020
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    40   58 from     0.14443     to     0.18984     ref=     5.6936    
 checkperc> Increasing con cutoff atoms    50   51 from     0.17925E-02 to     0.22973E-02 ref=     1.2319    
 checkperc> Increasing con cutoff atoms    51   53 from     0.76767E-02 to     0.82310E-02 ref=     3.1348    
 checkperc> Increasing con cutoff atoms    64   66 from     0.61697E-03 to     0.83500E-03 ref=     2.1605    
 checkperc> Increasing con cutoff atoms    67   71 from     0.12312E-02 to     0.12734E-02 ref=     2.4443    
 checkperc> Increasing con cutoff atoms    67   72 from     0.47146E-02 to     0.47822E-02 ref=     3.4149    
 checkperc> Increasing con cutoff atoms    68   72 from     0.57734E-02 to     0.60802E-02 ref=     4.3051    
 checkperc> Increasing con cutoff atoms    69   71 from     0.50293E-03 to     0.52867E-03 ref=     1.4086    
 checkperc> Increasing con cutoff atoms    70   71 from     0.79560E-03 to     0.80574E-03 ref=     2.1602    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1413 steps. Energy=    -450.3622777       time=      14.82
 Minus side of path:                    1307 steps. Energy=    -447.7566490       time=      13.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3622777  2.6917         -447.6705538 0.86095E-01     -447.7566490  38.343  37.506   3.390  64.311
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    38   42 from     0.22736E-01 to     0.28902E-01 ref=     2.4851    
 checkperc> Increasing con cutoff atoms    40   41 from     0.58505E-03 to     0.88780E-03 ref=     1.0903    
 checkperc> Increasing con cutoff atoms    40   43 from     0.12264E-01 to     0.13517E-01 ref=     2.1587    
 checkperc> Increasing con cutoff atoms    42   45 from     0.41415E-02 to     0.43103E-02 ref=     2.1592    
 checkperc> Increasing con cutoff atoms    43   44 from     0.11763E-01 to     0.14189E-01 ref=     2.1446    
 checkperc> Increasing con cutoff atoms    43   49 from     0.60221E-01 to     0.60167     ref=     2.2493    
 checkperc> Increasing con cutoff atoms    45   46 from     0.49061E-02 to     0.53732E-02 ref=     1.7653    
 checkperc> Increasing con cutoff atoms    68   72 from     0.60802E-02 to     0.60836E-02 ref=     4.3051    
 checkperc> Increasing con cutoff atoms    70   71 from     0.80574E-03 to     0.81064E-03 ref=     2.1602    
 checkperc> Increasing con cutoff atoms    40   41 from     0.88780E-03 to     0.10781E-02 ref=     1.0903    
 checkperc> Increasing con cutoff atoms    42   45 from     0.43103E-02 to     0.44347E-02 ref=     2.1592    
 checkperc> Increasing con cutoff atoms    42   47 from     0.40382E-02 to     0.47362E-02 ref=     2.1681    
 checkperc> Increasing con cutoff atoms    43   44 from     0.14189E-01 to     0.15602E-01 ref=     2.1446    
 checkperc> Increasing con cutoff atoms    65   66 from     0.70410E-03 to     0.73005E-03 ref=     1.0805    
 checkperc> Increasing con cutoff atoms    67   68 from     0.15316E-03 to     0.15538E-03 ref=     1.0826    
 checkperc> Increasing con cutoff atoms    69   70 from     0.18316E-03 to     0.19415E-03 ref=     1.0823    
 checkperc> Increasing con cutoff atoms   119  120 from     0.30788E-02 to     0.30829E-02 ref=     1.0882    
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1654 steps. Energy=    -451.5852727       time=      18.76
 Minus side of path:                    1801 steps. Energy=    -450.9727420       time=      21.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5852727  5.1758         -446.4095015  4.5632         -450.9727420  91.174  75.185   3.583  60.842
        Known (#3)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms   119  120 from     0.30829E-02 to     0.30890E-02 ref=     1.0882    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.13085E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.70     5     4        1.48     3 
 

 tryconnect> Interpolation for minima 2_F and 5_U 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=    32
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    770 fraction=    0.990000 images=     5 time=       1.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    795 steps, energy/image=     99.91151615     RMS=25.89376023     images=   6
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   55.03     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.5147018159E-01
 Double-ended search iterations= 560 RMS= 0.0335 Dev= 5.07% S= 63.13 time= 65.83
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  44.18
 isnewts> transition state is the same as number        3 energy=     -446.4095014647
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1359 steps. Energy=    -449.0668792       time=      14.25
 Minus side of path:                    1817 steps. Energy=    -450.9727420       time=      22.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0668792  2.6574         -446.4095015  4.5632         -450.9727420  57.991  53.100   4.993  43.657
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to S set.

 tryconnect> Interpolation for minima 3_S and 4_U 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     21 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     46 steps, energy/image=    -447.0284905     RMS=.4568338402     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   1.838     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0945 Dev= 0.83% S= 1.71 time= 1.04
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  21.70

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1247 steps. Energy=    -450.3622777       time=      12.44
 Minus side of path:                    1289 steps. Energy=    -451.5852726       time=      13.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3622777 0.50156         -449.8607177  1.7246         -451.5852726   1.750   1.483 177.550   1.228
        Known (#4)                                              Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.12828E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.37     7 
 

 tryconnect> Interpolation for minima 2_F and 7_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=    29
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    614 fraction=    0.990000 images=     4 time=       1.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    639 steps, energy/image=    -422.0538873     RMS=1.667361083     images=   5
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      2     7 dist=   52.27     Attempts, images and iterations=     0    15   525
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0411 Dev= 3.84% S= 58.92 time= 57.95
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=  51.30
 isnewts> transition state is the same as number        3 energy=     -446.4095014653
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.13608E+06
 decide> The unconnected minima in the chain and their distances are:
     2       51.38     6 
 

 tryconnect> Interpolation for minima 2_F and 6_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=    19
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    421 fraction=    0.990000 images=     5 time=       1.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    446 steps, energy/image=    -126.6597196     RMS=20.08241550     images=   6
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   54.76     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0114 Dev= 2.15% S= 54.62 time= 66.23
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=  29.47

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1471 steps. Energy=    -450.4708986       time=      16.39
 Minus side of path:                    1515 steps. Energy=    -450.9727420       time=      17.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4708986 0.93133         -449.5395712  1.4332         -450.9727420  55.968  51.441   2.035 107.125
        Known (#2)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -451.4537995  2.3395        -449.1143342  2.4709        -451.5852727  39.807  31.812   3.632  60.020
   3     -451.5852727  5.1758        -446.4095015  4.5632        -450.9727420  91.174  75.185   3.583  60.842
   6     -450.9727420  1.4332        -449.5395712 0.93133        -450.4708986  55.968  51.441   2.035 107.125

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                               857.58
 OPTIM> # of energy calls=                         10 time=           0.07 %=  0.0
 OPTIM> # of energy+gradient calls=             72363 time=         528.24 %= 61.6
 OPTIM> # of energy+gradient+Hessian calls=       530 time=         146.67 %= 17.1
