
 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 12:49:19
  [-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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -449.9056515     RMS force=    0.9946977436E-06
 OPTIM> Final energy  =    -452.8584337     RMS force=    0.9022991128E-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=     16154.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.28     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0498 Dev= 0.25% S= 26.26 time= 26.00
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        194
 DNEB run yielded 1 true transition state(s) time= 183.05

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1158 steps. Energy=    -451.5260661       time=      11.59
 Minus side of path:                    1287 steps. Energy=    -452.0566179       time=      13.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5260661 0.29088E-01     -451.4969781 0.55964         -452.0566179  12.333  11.637   4.634  47.045
        *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      2 steps with      2 missing connections, weight=     18528.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.67     3     3       23.52     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2398 Dev= 0.12% S= 18.28 time= 6.76
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=  39.98

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1200 steps. Energy=    -452.8611298       time=      12.20
 Minus side of path:                    1359 steps. Energy=    -452.6707347       time=      14.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8611298  2.3588         -450.5022876  2.1684         -452.6707347  20.495  17.229   1.941 112.310
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1962 Dev= 0.57% S= 24.31 time= 13.00
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        141
 DNEB run yielded 1 true transition state(s) time=  74.24

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1149 steps. Energy=    -449.9056515       time=      11.43
 Minus side of path:                    1085 steps. Energy=    -449.8146537       time=      10.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9056515 0.10131         -449.8043440 0.10310E-01     -449.8146537   7.160   7.070   3.206  68.001
        Known (#1)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     16314.    
 decide> The unconnected minima in the chain and their distances are:
     2        3.42     5     5       25.34     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0079 Dev= 0.00% S= 3.42 time= 1.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  18.84

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1174 steps. Energy=    -452.8611298       time=      11.70
 Minus side of path:                    1156 steps. Energy=    -452.8584337       time=      11.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8611298 0.36999E-02     -452.8574299 0.10038E-02     -452.8584337   3.447   3.418   7.375  29.559
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0767 Dev= 0.43% S= 26.19 time= 13.01
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        162
 DNEB run yielded 1 true transition state(s) time=  82.51

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1257 steps. Energy=    -452.0566179       time=      12.95
 Minus side of path:                    1255 steps. Energy=    -455.5630004       time=      12.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.0566179 0.36574         -451.6908794  3.8721         -455.5630004  28.597  24.891   2.281  95.578
        Known (#4)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     19129.    
 decide> The unconnected minima in the chain and their distances are:
     6       26.74     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 6_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 1.5564 Dev= 0.56% S= 28.57 time= 16.91
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         98
 DNEB run yielded 1 true transition state(s) time=  52.27
 isnewts> transition state is the same as number        3 energy=     -449.8043439740
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1166 steps. Energy=    -449.9056515       time=      11.64
 Minus side of path:                    1087 steps. Energy=    -449.8146537       time=      10.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9056515 0.10131         -449.8043440 0.10310E-01     -449.8146537   7.160   7.070   3.205  68.010
        Known (#1)                                              Known (#7)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     20790.    
 decide> The unconnected minima in the chain and their distances are:
     6       27.50     7 
 

 tryconnect> 280-iteration DNEB run for minima 6_F and 7_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0700 Dev= 0.41% S= 29.06 time= 16.91
 Following    1 images are candidates for TS:    4  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 122.22
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     20983.    
 decide> The unconnected minima in the chain and their distances are:
     6       15.59     3     3       25.81     7 
 

 tryconnect> 140-iteration DNEB run for minima 3_U and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1036 Dev= 0.08% S= 15.72 time= 4.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  32.75

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1137 steps. Energy=    -451.5260661       time=      11.34
 Minus side of path:                    1305 steps. Energy=    -452.6707347       time=      13.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5260661 0.16362E-01     -451.5097037  1.1610         -452.6707347  16.932  15.599   5.405  40.333
        Known (#3)                                              Known (#6)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 3_F and 7_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1440 Dev= 0.22% S= 26.53 time= 13.00
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=  49.91

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1334 steps. Energy=    -449.9056515       time=      14.15
 Minus side of path:                    1644 steps. Energy=    -451.9541496       time=      19.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9056515 0.98513         -448.9205240  3.0336         -451.9541496  37.314  33.840   2.235  97.530
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     20750.    
 decide> The unconnected minima in the chain and their distances are:
     4       27.48     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1129 Dev= 0.18% S= 29.01 time= 16.90
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=  39.54

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1209 steps. Energy=    -449.9056515       time=      12.25
 Minus side of path:                    1470 steps. Energy=    -455.5630004       time=      16.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9056515  1.2951         -448.6105027  6.9525         -455.5630004  42.873  38.285   2.599  83.890
        Known (#1)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   9     -449.9056515  1.2951        -448.6105027  6.9525        -455.5630004  42.873  38.285   2.599  83.890
   5     -455.5630004  3.8721        -451.6908794 0.36574        -452.0566179  28.597  24.891   2.281  95.578
   1     -452.0566179 0.55964        -451.4969781 0.29088E-01    -451.5260661  12.333  11.637   4.634  47.045
   7     -451.5260661 0.16362E-01    -451.5097037  1.1610        -452.6707347  16.932  15.599   5.405  40.333
   2     -452.6707347  2.1684        -450.5022876  2.3588        -452.8611298  20.495  17.229   1.941 112.310
   4     -452.8611298 0.36999E-02    -452.8574299 0.10038E-02    -452.8584337   3.447   3.418   7.375  29.559

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                              1055.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             51151 time=         400.68 %= 37.9
 OPTIM> # of energy+gradient+Hessian calls=      1143 time=         367.17 %= 34.8
