
 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 05/24/2012 at 11:44:41
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    17
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>  321 Cartesian coordinates will be optimised for  107 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
 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> 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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.9683128     RMS force=    0.9527730669E-06
 OPTIM> Final energy  =    -535.5515772     RMS force=    0.9861479562E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     6142.1    
 decide> The unconnected minima in the chain and their distances are:
     2       18.31     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 1.3143 Dev= 1.44% S= 22.96 time= 1.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   9.04

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     643 steps. Energy=    -537.1728982       time=       1.60
 Minus side of path:                     626 steps. Energy=    -536.0534499       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.1728982  1.5633         -535.6095818 0.44387         -536.0534499   5.951   5.511  10.646  10.051
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     7101.9    
 decide> The unconnected minima in the chain and their distances are:
     2       13.42     4     3       16.73     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 1.0652 Dev= 0.25% S= 18.15 time= 1.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=   5.17

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     686 steps. Energy=    -536.0534499       time=       1.80
 Minus side of path:                     682 steps. Energy=    -533.9909644       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0534499  2.3830         -533.6704048 0.32056         -533.9909644  16.815  12.031   7.985  13.399
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1751 Dev= 0.27% S= 18.05 time= 1.88
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         88
 DNEB run yielded 1 true transition state(s) time=   8.78

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     712 steps. Energy=    -533.9683128       time=       1.82
 Minus side of path:                     659 steps. Energy=    -533.7204411       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9683128 0.27733         -533.6909865 0.29455E-01     -533.7204411   8.276   7.808   5.536  19.327
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     4119.2    
 decide> The unconnected minima in the chain and their distances are:
     2       11.16     5     3       13.98     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0816 Dev= 0.06% S= 11.31 time= 0.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.11

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     731 steps. Energy=    -536.2208487       time=       1.85
 Minus side of path:                     626 steps. Energy=    -533.9909644       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.2208487  2.3724         -533.8484413 0.14252         -533.9909644  13.182  11.439   5.742  18.634
        *NEW* (Placed in 7)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 3_U and 6_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.5817 Dev= 0.49% S= 14.78 time= 1.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         86
 DNEB run yielded 1 true transition state(s) time=   8.41
 isnewts> transition state is the same as number        3 energy=     -533.6909865490
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     711 steps. Energy=    -533.9683128       time=       1.84
 Minus side of path:                     642 steps. Energy=    -533.7204411       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9683128 0.27733         -533.6909865 0.29455E-01     -533.7204411   8.276   7.808   5.539  19.318
        Known (#1)                                              Known (#6)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     6042.5    
 decide> The unconnected minima in the chain and their distances are:
     2       12.49     7     4       16.00     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2641 Dev= 0.14% S= 12.76 time= 0.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     613 steps. Energy=    -535.5515772       time=       1.52
 Minus side of path:                     721 steps. Energy=    -536.2208487       time=       1.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5515772 0.33437         -535.2172092  1.0036         -536.2208487  13.771  12.496   5.564  19.232
        Known (#2)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 4_F and 6_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2516 Dev= 0.48% S= 16.90 time= 1.24
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   6.81
 isnewts> transition state is the same as number        3 energy=     -533.6909865496
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5461.0    
 decide> The unconnected minima in the chain and their distances are:
     3       13.98     6 
 

 tryconnect> 805-iteration DNEB run for minima 3_F and 6_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      45.38039494    
 Double-ended search iterations= 805 RMS= 0.5227 Dev= 3.61% S= 15.76 time= 37.40
 Following    2 images are candidates for TS:    9   18  
 Converged to TS (number of iterations):         18
 Converged to TS (number of iterations):         64
 DNEB run yielded 2 true transition state(s) time=   9.20
 isnewts> transition state is the same as number        3 energy=     -533.6909865488
 tryconnect> Will not repeat search for TS      2 same as TS      3

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     636 steps. Energy=    -537.4643304       time=       1.57
 Minus side of path:                     630 steps. Energy=    -537.1728982       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.4643304  8.4076         -529.0567193  8.1162         -537.1728982   4.382   3.600  17.945   5.963
        *NEW* (Placed in 8)                                     Known (#3)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     3832.5    
 decide> The unconnected minima in the chain and their distances are:
     8       15.65     6 
 

 tryconnect> 140-iteration DNEB run for minima 6_S and 8_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1564 Dev= 0.16% S= 16.13 time= 1.24
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.69
 isnewts> transition state is the same as number        3 energy=     -533.6909865492
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     5827.2    
 decide> The unconnected minima in the chain and their distances are:
     5       18.00     6 
 

 tryconnect> 175-iteration DNEB run for minima 5_F and 6_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3291 Dev= 0.57% S= 20.09 time= 1.88
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   6.03
 isnewts> transition state is the same as number        1 energy=     -535.6095818186
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     655 steps. Energy=    -537.1728982       time=       1.62
 Minus side of path:                     611 steps. Energy=    -536.0534499       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.1728982  1.5633         -535.6095818 0.44387         -536.0534499   5.951   5.511  10.614  10.081
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     6028.5    
 decide> The unconnected minima in the chain and their distances are:
     4       18.20     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2370 Dev= 0.38% S= 19.66 time= 1.88
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  24.47
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 8 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     6424.3    
 decide> The unconnected minima in the chain and their distances are:
     8       18.59     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 8_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0998 Dev= 0.31% S= 19.86 time= 1.88
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=   9.85

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     609 steps. Energy=    -533.7204411       time=       1.48
 Minus side of path:                    1046 steps. Energy=    -537.4643304       time=       2.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.7204411 0.38685E-03     -533.7200542  3.7443         -537.4643304  15.939  15.651   2.591  41.294
        Known (#6)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -533.9683128 0.27733        -533.6909865 0.29455E-01    -533.7204411   8.276   7.808   5.536  19.327
   9     -533.7204411 0.38685E-03    -533.7200542  3.7443        -537.4643304  15.939  15.651   2.591  41.294
   7     -537.4643304  8.4076        -529.0567193  8.1162        -537.1728982   4.382   3.600  17.945   5.963
   1     -537.1728982  1.5633        -535.6095818 0.44387        -536.0534499   5.951   5.511  10.646  10.051
   2     -536.0534499  2.3830        -533.6704048 0.32056        -533.9909644  16.815  12.031   7.985  13.399
   4     -533.9909644 0.14252        -533.8484413  2.3724        -536.2208487  13.182  11.439   5.742  18.634
   6     -536.2208487  1.0036        -535.2172092 0.33437        -535.5515772  13.771  12.496   5.564  19.232

 Number of TS in the path       =      7
 Number of cycles               =      9

 Elapsed time=                               188.19
 OPTIM> # of energy calls=                        140 time=           0.28 %=  0.1
 OPTIM> # of energy+gradient calls=             48904 time=          97.14 %= 51.6
 OPTIM> # of energy+gradient+Hessian calls=      1002 time=          54.13 %= 28.8
