
 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 21:38:32
  [-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>> 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=    -442.2167612     RMS force=    0.9482654627E-06
 OPTIM> Final energy  =    -452.7143081     RMS force=    0.8726195807E-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=    0.14275E+07
 decide> The unconnected minima in the chain and their distances are:
     2      112.60     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Cold fusion diagnosed - step discarded, energy, limit=    -2356092.752        -1000000.000    
 lbfgs> Final DNEB force constant      43.21942375    
 Double-ended search iterations= 324 RMS= 1110728430495.6250 Dev= 5.50% S= 302.21 time= 20.62
 Following    4 images are candidates for TS:    5   14   16   22  
 Converged to TS (number of iterations):        148
 Converged to TS (number of iterations):         91
 Converged to TS (number of iterations):        104
 Converged to TS (number of iterations):        163
 DNEB run yielded 4 true transition state(s) time= 332.79
 tryconnect> Transition state with energy     -383.5887305     ignored

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1321 steps. Energy=    -449.3659220       time=      14.84
 Minus side of path:                    1289 steps. Energy=    -453.1855420       time=      13.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3659220  1.6541         -447.7118405  5.4737         -453.1855420  29.966  26.166  13.841  15.750
        *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:                    1106 steps. Energy=    -451.7545398       time=      11.01
 Minus side of path:                    1214 steps. Energy=    -451.2821906       time=      12.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7545398  1.0854         -450.6691619 0.61303         -451.2821906   1.844   1.643 167.310   1.303
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1253 steps. Energy=    -452.4704859       time=      13.17
 Minus side of path:                    1436 steps. Energy=    -452.7143081       time=      15.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4704859 0.87353E-01     -452.3831326 0.33118         -452.7143081  20.534  18.112   2.146 101.563
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.10458E+07
 decide> The unconnected minima in the chain and their distances are:
     7       20.77     4     3      101.21     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_U and 7_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0806 Dev= 0.09% S= 21.06 time= 9.78
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=  47.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1490 steps. Energy=    -452.7143081       time=      20.95
 Minus side of path:                    1497 steps. Energy=    -453.1855420       time=      21.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.7143081 0.46497         -452.2493393 0.93620         -453.1855420  37.274  21.095   4.281  50.926
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 805 RMS= 0.2280 Dev= 1.41% S= 118.30 time= 141.28
 Following    1 images are candidates for TS:   11  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 127.65
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.12165E+07
 decide> The unconnected minima in the chain and their distances are:
     4      106.75     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      17.10339358    
 Double-ended search iterations= 847 RMS= 0.5441 Dev= 0.31% S= 126.43 time= 147.40
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        112
 DNEB run yielded 1 true transition state(s) time=  75.72

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1295 steps. Energy=    -445.1308187       time=      15.01
 Minus side of path:                    1313 steps. Energy=    -448.9641219       time=      15.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.1308187  1.6579         -443.4728876  5.4912         -448.9641219  30.282  26.578  13.970  15.604
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.36669E+06
 decide> The unconnected minima in the chain and their distances are:
     4       53.89     9     8       59.46     1 
 

 tryconnect> 560-iteration DNEB run for minima 4_F and 9_U using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0651 Dev= 2.52% S= 60.22 time= 69.25
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  50.09

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1291 steps. Energy=    -448.9641219       time=      15.67
 Minus side of path:                    1551 steps. Energy=    -453.1923869       time=      18.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.9641219 0.22348         -448.7406429  4.4517         -453.1923869  53.147  49.724   1.938 112.468
        Known (#9)                                              *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 595-iteration DNEB run for minima 1_S and 8_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.1039 Dev= 3.76% S= 68.30 time= 76.21
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):         92
 Converged to TS (number of iterations):        105
 DNEB run yielded 2 true transition state(s) time= 110.08

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    2597 steps. Energy=    -446.0519807       time=      46.74
 Minus side of path:                    1406 steps. Energy=    -442.2167612       time=      19.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0519807  5.2664         -440.7855415  1.4312         -442.2167612 110.878 100.177   1.573 138.579
        *NEW* (Placed in 11)                                    Known (#1)
 Unconnected minimum 11 found its way to S set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1394 steps. Energy=    -442.6746751       time=      18.09
 Minus side of path:                    2531 steps. Energy=    -446.4956055       time=      50.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -442.6746751  1.4305         -441.2441783  5.2514         -446.4956055 110.950 100.233   1.577 138.264
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 13 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     17575.    
 decide> The unconnected minima in the chain and their distances are:
     3       26.00    11 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 11_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0546 Dev= 0.51% S= 27.33 time= 13.38
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  38.04

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1268 steps. Energy=    -446.0519807       time=      17.56
 Minus side of path:                    1269 steps. Energy=    -446.0868643       time=      15.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0519807 0.46622         -445.5857583 0.50111         -446.0868643  10.109   9.395   2.731  79.836
        Known (#11)                                             *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     10730.    
 decide> The unconnected minima in the chain and their distances are:
     3       22.06    14 
 

 tryconnect> 210-iteration DNEB run for minima 3_F and 14_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0588 Dev= 0.43% S= 22.58 time= 10.00
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=  58.89

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1250 steps. Energy=    -448.4321458       time=      13.82
 Minus side of path:                    1449 steps. Energy=    -449.3659220       time=      16.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4321458 0.23000         -448.2021416  1.1638         -449.3659220  18.391  13.425   2.901  75.152
        *NEW* (Placed in 15)                                    Known (#3)
 Unconnected minimum 15 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 15 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     5910.0    
 decide> The unconnected minima in the chain and their distances are:
    15       18.08    14 
 

 tryconnect> 175-iteration DNEB run for minima 14_S and 15_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0862 Dev= 1.41% S= 18.57 time= 6.89
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=  37.61

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1279 steps. Energy=    -448.4321458       time=      14.30
 Minus side of path:                    1256 steps. Energy=    -446.0868643       time=      13.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4321458  2.5347         -445.8974951 0.18937         -446.0868643  20.101  18.082   4.729  46.097
        Known (#15)                                             Known (#14)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -442.2167612  1.4312        -440.7855415  5.2664        -446.0519807 110.878 100.177   1.573 138.579
   9     -446.0519807 0.46622        -445.5857583 0.50111        -446.0868643  10.109   9.395   2.731  79.836
  11     -446.0868643 0.18937        -445.8974951  2.5347        -448.4321458  20.101  18.082   4.729  46.097
  10     -448.4321458 0.23000        -448.2021416  1.1638        -449.3659220  18.391  13.425   2.901  75.152
   1     -449.3659220  1.6541        -447.7118405  5.4737        -453.1855420  29.966  26.166  13.841  15.750
   4     -453.1855420 0.93620        -452.2493393 0.46497        -452.7143081  37.274  21.095   4.281  50.926

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

 Elapsed time=                              1788.81
 OPTIM> # of energy calls=                        252 time=           1.90 %=  0.1
 OPTIM> # of energy+gradient calls=            117309 time=         881.11 %= 49.3
 OPTIM> # of energy+gradient+Hessian calls=      1421 time=         417.44 %= 23.3
