
 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 21:45:29
  [-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> 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
 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 =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -453.0685383     RMS force=    0.9502767284E-06
 OPTIM> Final energy  =    -454.0602536     RMS force=    0.9990932197E-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=    0.16677E+06
 decide> The unconnected minima in the chain and their distances are:
     2       55.04     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 2_F using 16 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 560 RMS= 0.0420 Dev= 5.50% S= 68.08 time= 67.01
 Following    2 images are candidates for TS:    9   11  
 Converged to TS (number of iterations):        247
 Converged to TS (number of iterations):        115
 DNEB run yielded 2 true transition state(s) time= 184.79

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1731 steps. Energy=    -459.8346797       time=      20.56
 Minus side of path:                    1540 steps. Energy=    -453.9442338       time=      17.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -459.8346797  8.2579         -451.5767569  2.3675         -453.9442338  84.178  67.388   2.129 102.390
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1208 steps. Energy=    -447.5540480       time=      12.19
 Minus side of path:                    1514 steps. Energy=    -453.4916410       time=      16.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5540480 0.43919E-01     -447.5101291  5.9815         -453.4916410  24.371  21.809   2.309  94.413
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     74993.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.37     5     6       39.41     3     4       10.13     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0446 Dev= 0.55% S= 24.05 time= 12.91
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=  32.86

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1159 steps. Energy=    -447.5540480       time=      11.51
 Minus side of path:                    1372 steps. Energy=    -453.6863785       time=      14.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5540480 0.11208E-02     -447.5529272  6.1335         -453.6863785  32.819  32.569   1.909 114.200
        Known (#5)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 3_U and 6_U using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.1079 Dev= 3.09% S= 49.44 time= 31.76
 Following    3 images are candidates for TS:    4    7   11  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         66
 Converged to TS (number of iterations):         23
 DNEB run yielded 3 true transition state(s) time=  82.67

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1260 steps. Energy=    -460.7691167       time=      12.99
 Minus side of path:                    1140 steps. Energy=    -459.8346796       time=      11.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.7691167  2.3044         -458.4647028  1.3700         -459.8346796  27.049  21.327   3.688  59.114
        *NEW* (Placed in 8)                                     Known (#3)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1036 steps. Energy=    -454.9306062       time=       9.88
 Minus side of path:                    1652 steps. Energy=    -460.0130763       time=      19.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.9306062 0.39797         -454.5326364  5.4804         -460.0130763  26.433  24.441   2.311  94.348
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1059 steps. Energy=    -454.9306062       time=      10.19
 Minus side of path:                    1049 steps. Energy=    -453.4916410       time=      10.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.9306062  2.0738         -452.8568006 0.63484         -453.4916410   9.382   8.675   3.648  59.758
        Known (#9)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0614 Dev= 0.16% S= 10.21 time= 2.41
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=  21.49

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1252 steps. Energy=    -453.0685383       time=      12.82
 Minus side of path:                    1281 steps. Energy=    -453.9906852       time=      13.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.0685383 0.14894         -452.9195970  1.0711         -453.9906852  11.722  10.940   3.316  65.743
        Known (#1)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      3 missing connections, weight=     21515.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.99     7    10       21.07     8     4        2.66    11 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 7_U using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0292 Dev= 0.12% S= 23.20 time= 9.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  22.89

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1125 steps. Energy=    -453.6863785       time=      11.08
 Minus side of path:                    1124 steps. Energy=    -454.0602536       time=      11.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6863785 0.79967         -452.8867126  1.1735         -454.0602536  24.875  22.993   2.693  80.966
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 8_U and 10_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 210 RMS= 0.0637 Dev= 0.23% S= 21.33 time= 9.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=  41.64

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1081 steps. Energy=    -460.7318980       time=      10.50
 Minus side of path:                    1072 steps. Energy=    -460.0130763       time=      10.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.7318980  1.1685         -459.5633810 0.44970         -460.0130763  16.594  14.606   4.590  47.495
        *NEW* (Placed in 12)                                    Known (#10)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 11_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0125 Dev= 0.09% S= 2.66 time= 1.08
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  20.54

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1255 steps. Energy=    -453.9906852       time=      13.01
 Minus side of path:                    1264 steps. Energy=    -453.9442338       time=      13.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.9906852 0.50756E-01     -453.9399292 0.43047E-02     -453.9442338   2.671   2.662   2.840  76.761
        Known (#11)                                             Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      1 missing connections, weight=     4546.0    
 decide> The unconnected minima in the chain and their distances are:
    12       16.57     8 
 

 tryconnect> 140-iteration DNEB run for minima 8_S and 12_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0379 Dev= 0.07% S= 16.72 time= 4.26
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  24.24

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1046 steps. Energy=    -460.7691167       time=      10.13
 Minus side of path:                    1057 steps. Energy=    -460.7318980       time=      10.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.7691167 0.84132         -459.9278010 0.80410         -460.7318980  17.430  16.568   6.282  34.700
        Known (#8)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -453.0685383 0.14894        -452.9195970  1.0711        -453.9906852  11.722  10.940   3.316  65.743
  10     -453.9906852 0.50756E-01    -453.9399292 0.43047E-02    -453.9442338   2.671   2.662   2.840  76.761
   1     -453.9442338  2.3675        -451.5767569  8.2579        -459.8346797  84.178  67.388   2.129 102.390
   4     -459.8346797  1.3700        -458.4647028  2.3044        -460.7691167  27.049  21.327   3.688  59.114
  11     -460.7691167 0.84132        -459.9278010 0.80410        -460.7318980  17.430  16.568   6.282  34.700
   9     -460.7318980  1.1685        -459.5633810 0.44970        -460.0130763  16.594  14.606   4.590  47.495
   5     -460.0130763  5.4804        -454.5326364 0.39797        -454.9306062  26.433  24.441   2.311  94.348
   6     -454.9306062  2.0738        -452.8568006 0.63484        -453.4916410   9.382   8.675   3.648  59.758
   2     -453.4916410  5.9815        -447.5101291 0.43919E-01    -447.5540480  24.371  21.809   2.309  94.413
   3     -447.5540480 0.11208E-02    -447.5529272  6.1335        -453.6863785  32.819  32.569   1.909 114.200
   8     -453.6863785 0.79967        -452.8867126  1.1735        -454.0602536  24.875  22.993   2.693  80.966

 Number of TS in the path       =     11
 Number of cycles               =      4

 Elapsed time=                               852.72
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             59224 time=         438.90 %= 51.5
 OPTIM> # of energy+gradient+Hessian calls=       723 time=         200.29 %= 23.5
