
 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 21:17:23
  [-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=    -449.4375602     RMS force=    0.8620378795E-06
 OPTIM> Final energy  =    -449.1932966     RMS force=    0.8634156912E-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=     41808.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.71     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 350 RMS= 0.2514 Dev= 0.69% S= 40.70 time= 25.76
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  40.92

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1313 steps. Energy=    -448.7668857       time=      14.77
 Minus side of path:                    1338 steps. Energy=    -449.6369359       time=      16.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7668857  3.1073         -445.6596341  3.9773         -449.6369359   8.968   7.740  30.658   7.111
        *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=     29043.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.19     3     3       11.51     1 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 3_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 315 RMS= 0.1543 Dev= 1.38% S= 33.72 time= 21.27
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=  39.59

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1372 steps. Energy=    -448.7668858       time=      17.12
 Minus side of path:                    1553 steps. Energy=    -449.3451071       time=      22.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7668858  3.3812         -445.3857099  3.9594         -449.3451071  39.098  32.465   5.614  38.835
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.7194 Dev= 1.07% S= 12.29 time= 2.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  33.54

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1267 steps. Energy=    -449.2939608       time=      16.19
 Minus side of path:                    1327 steps. Energy=    -450.1686935       time=      18.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2939608  3.1039         -446.1901040  3.9786         -450.1686935   8.987   7.763  30.700   7.101
        *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      6 steps with      3 missing connections, weight=     26824.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.52     5     4        8.06     7     6        8.26     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 5_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0218 Dev= 0.12% S= 30.24 time= 17.10
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=  33.49

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1355 steps. Energy=    -449.3451071       time=      17.95
 Minus side of path:                    1322 steps. Energy=    -449.1932966       time=      17.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3451071 0.43119         -448.9139142 0.27938         -449.1932966  31.408  29.552   3.436  63.455
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0445 Dev= 0.01% S= 8.08 time= 1.10
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  31.63

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1359 steps. Energy=    -450.1686935       time=      17.56
 Minus side of path:                    1267 steps. Energy=    -449.6369359       time=      13.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.1686935 0.53296         -449.6357384 0.11975E-02     -449.6369359   8.380   8.060   4.762  45.776
        Known (#7)                                              Known (#4)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3515 Dev= 0.26% S= 8.96 time= 1.06
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  34.80
 isnewts> transition state is the same as number        3 energy=     -446.1901040150
 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:                    1271 steps. Energy=    -449.2939608       time=      15.97
 Minus side of path:                    1324 steps. Energy=    -450.1686935       time=      19.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2939608  3.1039         -446.1901040  3.9786         -450.1686935   8.987   7.762  30.743   7.091
        Known (#6)                                              Known (#7)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1127.8    
 decide> The unconnected minima in the chain and their distances are:
     6        8.26     1 
 

 tryconnect> 665-iteration DNEB run for minima 1_S and 6_F using 19 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      12.76281562    
 Double-ended search iterations= 665 RMS= 0.0537 Dev= 2.74% S= 10.33 time= 94.71
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  30.72
 isnewts> transition state is the same as number        3 energy=     -446.1901040235
 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=     1691.6    
 decide> The unconnected minima in the chain and their distances are:
     6        8.26     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 6_F using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 805 RMS= 0.0473 Dev= 3.71% S= 11.66 time= 138.39
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  28.92
 isnewts> transition state is the same as number        3 energy=     -446.1901040402
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2202.6    
 decide> The unconnected minima in the chain and their distances are:
     7       13.01     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 7_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5126 Dev= 0.27% S= 14.08 time= 2.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  30.80

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1306 steps. Energy=    -449.4375602       time=      15.26
 Minus side of path:                    1346 steps. Energy=    -450.1686935       time=      15.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.4375602  2.2185         -447.2190359  2.9497         -450.1686935  17.248  13.032  19.776  11.023
        Known (#1)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -449.4375602  2.2185        -447.2190359  2.9497        -450.1686935  17.248  13.032  19.776  11.023
   5     -450.1686935 0.53296        -449.6357384 0.11975E-02    -449.6369359   8.380   8.060   4.762  45.776
   1     -449.6369359  3.9773        -445.6596341  3.1073        -448.7668857   8.968   7.740  30.658   7.111
   2     -448.7668857  3.3812        -445.3857099  3.9594        -449.3451071  39.098  32.465   5.614  38.835
   4     -449.3451071 0.43119        -448.9139142 0.27938        -449.1932966  31.408  29.552   3.436  63.455

 Number of TS in the path       =      5
 Number of cycles               =      6

 Elapsed time=                               848.48
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             71518 time=         532.85 %= 62.8
 OPTIM> # of energy+gradient+Hessian calls=       364 time=         108.40 %= 12.8
