
 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 05/23/2012 at 21:09:02
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -452.9214863     RMS force=    0.9560088160E-06
 OPTIM> Final energy  =    -455.3846835     RMS force=    0.9893635764E-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=    0.17849E+06
 decide> The unconnected minima in the chain and their distances are:
     2       56.30     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 2_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5147018159E-01
 Double-ended search iterations= 560 RMS= 0.0643 Dev= 4.62% S= 73.02 time= 67.30
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        130
 DNEB run yielded 1 true transition state(s) time=  73.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1751 steps. Energy=    -454.3529882       time=      26.05
 Minus side of path:                    1742 steps. Energy=    -452.9214863       time=      23.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.3529882  4.5718         -449.7811769  3.1403         -452.9214863  75.054  63.178   1.996 109.233
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.21382E+06
 decide> The unconnected minima in the chain and their distances are:
     2       59.80     3 
 

 tryconnect> 595-iteration DNEB run for minima 2_F and 3_S using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 595 RMS= 0.0540 Dev= 5.09% S= 73.55 time= 75.58
 Following    2 images are candidates for TS:    8   11  
 Converged to TS (number of iterations):         48
 Converged to TS (number of iterations):        235
 DNEB run yielded 2 true transition state(s) time= 158.54

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1254 steps. Energy=    -455.5833838       time=      13.42
 Minus side of path:                    1285 steps. Energy=    -454.4300765       time=      14.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5833838  1.9753         -453.6080923 0.82198         -454.4300765  16.899  13.263   2.970  73.396
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1272 steps. Energy=    -452.3677826       time=      14.85
 Minus side of path:                    2744 steps. Energy=    -456.9270789       time=      52.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.3677826 0.41338E-01     -452.3264448  4.6006         -456.9270789  79.985  76.734   1.886 115.562
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     62360.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.27     6     7       24.46     3 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 6_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1024 Dev= 2.12% S= 46.27 time= 26.48
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        195
 DNEB run yielded 1 true transition state(s) time= 103.39
 isnewts> transition state is the same as number        3 energy=     -452.3264447508
 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:                    2327 steps. Energy=    -454.3529882       time=      41.44
 Minus side of path:                    1294 steps. Energy=    -452.3677826       time=      14.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.3529882  2.0265         -452.3264448 0.41338E-01     -452.3677826  67.719  65.001   1.888 115.454
        Known (#3)                                              Known (#6)
 Unconnected minimum 6 found its way to S set.

 tryconnect> 245-iteration DNEB run for minima 3_S and 7_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0303 Dev= 0.32% S= 24.92 time= 12.93
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=  45.93

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1231 steps. Energy=    -454.3529882       time=      13.19
 Minus side of path:                    1332 steps. Energy=    -456.9270789       time=      14.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.3529882 0.59822E-01     -454.2931667  2.6339         -456.9270789  25.844  24.463   3.182  68.515
        Known (#3)                                              Known (#7)
 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      4 steps with      2 missing connections, weight=     67370.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.42     5     4       18.28     3 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 5_U using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0469 Dev= 0.98% S= 41.29 time= 31.80
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=  57.16

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1274 steps. Energy=    -454.4300765       time=      15.53
 Minus side of path:                    1313 steps. Energy=    -455.6714146       time=      16.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.4300765 0.38821         -454.0418675  1.6295         -455.6714146  27.872  25.865   3.166  68.847
        Known (#5)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 3_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1393 Dev= 0.93% S= 19.93 time= 6.69
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=  47.61

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1251 steps. Energy=    -455.5833838       time=      13.89
 Minus side of path:                    1687 steps. Energy=    -456.0792424       time=      20.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5833838  2.8357         -452.7476410  3.3316         -456.0792424  42.878  36.957   2.995  72.779
        Known (#4)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     13517.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.11     8     9       10.55     7 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 8_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0321 Dev= 0.06% S= 23.40 time= 9.44
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=  36.84

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1289 steps. Energy=    -455.6714146       time=      16.59
 Minus side of path:                    1253 steps. Energy=    -455.3846835       time=      16.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.6714146 0.60912         -455.0622985 0.32239         -455.3846835  24.566  23.111   2.872  75.910
        Known (#8)                                              Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 7_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2501 Dev= 1.37% S= 11.82 time= 2.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  27.96

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1238 steps. Energy=    -456.9270789       time=      15.53
 Minus side of path:                    1179 steps. Energy=    -456.0792424       time=      15.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.9270789  7.1862         -449.7408761  6.3384         -456.0792424  14.045  10.550   6.234  34.967
        Known (#7)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -452.9214863  3.1403        -449.7811769  4.5718        -454.3529882  75.054  63.178   1.996 109.233
   4     -454.3529882  2.0265        -452.3264448 0.41338E-01    -452.3677826  67.719  65.001   1.888 115.454
   3     -452.3677826 0.41338E-01    -452.3264448  4.6006        -456.9270789  79.985  76.734   1.886 115.562
   9     -456.9270789  7.1862        -449.7408761  6.3384        -456.0792424  14.045  10.550   6.234  34.967
   7     -456.0792424  3.3316        -452.7476410  2.8357        -455.5833838  42.878  36.957   2.995  72.779
   2     -455.5833838  1.9753        -453.6080923 0.82198        -454.4300765  16.899  13.263   2.970  73.396
   6     -454.4300765 0.38821        -454.0418675  1.6295        -455.6714146  27.872  25.865   3.166  68.847
   8     -455.6714146 0.60912        -455.0622985 0.32239        -455.3846835  24.566  23.111   2.872  75.910

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                              1143.48
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             70313 time=         528.33 %= 46.2
 OPTIM> # of energy+gradient+Hessian calls=       950 time=         275.12 %= 24.1
