
 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 21:40:48
  [-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=    -450.6031786     RMS force=    0.9357517948E-06
 OPTIM> Final energy  =    -450.0049219     RMS force=    0.9959900755E-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=    0.12818E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.42     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 525 RMS= 0.0931 Dev= 5.07% S= 68.01 time= 60.12
 Following    2 images are candidates for TS:    8   12  
 Converged to TS (number of iterations):         96
 Converged to TS (number of iterations):         30
 DNEB run yielded 2 true transition state(s) time=  95.06

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1456 steps. Energy=    -446.8959712       time=      20.75
 Minus side of path:                    1576 steps. Energy=    -451.0647109       time=      25.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8959712  2.7246         -444.1714018  6.8933         -451.0647109  61.299  51.894   5.828  37.406
        *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=    -450.0049219       time=      16.06
 Minus side of path:                    1280 steps. Energy=    -451.0647109       time=      17.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.0049219  2.2166         -447.7883684  3.2763         -451.0647109   6.662   5.758  42.407   5.141
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     15999.    
 decide> The unconnected minima in the chain and their distances are:
     3       25.20     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1499 Dev= 4.02% S= 30.28 time= 13.34
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        115
 DNEB run yielded 1 true transition state(s) time=  63.22

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1304 steps. Energy=    -446.7561077       time=      13.83
 Minus side of path:                    1276 steps. Energy=    -446.8959712       time=      13.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.7561077 0.14356E-01     -446.7417521 0.15422         -446.8959712  16.361  16.087   5.655  38.547
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     9958.0    
 decide> The unconnected minima in the chain and their distances are:
     5       21.51     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 332 RMS= 1.0813 Dev= 0.85% S= 108.52 time= 15.27
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=  55.66

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1308 steps. Energy=    -449.9710327       time=      14.15
 Minus side of path:                    1286 steps. Energy=    -448.9404302       time=      13.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9710327  7.0844         -442.8866637  6.0538         -448.9404302  14.749  10.226  14.405  15.133
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     19916.    
 decide> The unconnected minima in the chain and their distances are:
     5       21.51     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 805 RMS= 0.0246 Dev= 4.95% S= 154.29 time= 141.09
 Following    4 images are candidates for TS:    7   13   18   22  
 Converged to TS (number of iterations):         96
 Converged to TS (number of iterations):        100
 Converged to TS (number of iterations):        199
 Converged to TS (number of iterations):         57
 DNEB run yielded 4 true transition state(s) time= 267.92

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1561 steps. Energy=    -450.5373870       time=      19.03
 Minus side of path:                    1552 steps. Energy=    -450.6031786       time=      18.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.5373870  3.0319         -447.5054453  3.0977         -450.6031786  74.408  49.573   3.834  56.865
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1414 steps. Energy=    -450.4566997       time=      16.75
 Minus side of path:                    1365 steps. Energy=    -449.9710327       time=      16.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4566997 0.82351         -449.6331861 0.33785         -449.9710327  36.947  35.777   3.075  70.895
        *NEW* (Placed in 9)                                     Known (#6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1300 steps. Energy=    -447.3628715       time=      16.40
 Minus side of path:                    1296 steps. Energy=    -447.3711305       time=      16.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3628715 0.12182         -447.2410471 0.13008         -447.3711305  19.647  18.547   3.458  63.034
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1296 steps. Energy=    -446.7561077       time=      17.09
 Minus side of path:                    1331 steps. Energy=    -447.3481762       time=      17.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.7561077 0.15369         -446.6024173 0.74576         -447.3481762  28.833  25.092   7.040  30.967
        Known (#5)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     30388.    
 decide> The unconnected minima in the chain and their distances are:
     4       31.02     7     9        8.17     8 
 

 tryconnect> 315-iteration DNEB run for minima 4_F and 7_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0744 Dev= 3.53% S= 36.95 time= 22.22
 Following    1 images are candidates for TS:    5  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 126.94

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2594 Dev= 0.18% S= 8.72 time= 1.33
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  23.25

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1309 steps. Energy=    -450.4566997       time=      14.11
 Minus side of path:                    1295 steps. Energy=    -450.5373870       time=      14.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4566997  3.6604         -446.7963160  3.7411         -450.5373870   9.393   8.166  29.501   7.390
        Known (#9)                                              Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     31254.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.50     7 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 7_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1022 Dev= 3.48% S= 38.14 time= 21.76
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         34
 DNEB run yielded 2 true transition state(s) time=  57.52
 isnewts> transition state is the same as number        2 energy=     -447.7883683367
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1256 steps. Energy=    -451.0647109       time=      13.91
 Minus side of path:                    1310 steps. Energy=    -450.0049219       time=      13.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0647109  3.2763         -447.7883683  2.2166         -450.0049219   7.938   6.597  19.087  11.421
        Known (#4)                                              Known (#2)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1283 steps. Energy=    -447.8979489       time=      13.66
 Minus side of path:                    1344 steps. Energy=    -451.0647109       time=      14.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8979489  6.0894         -441.8085026  9.2562         -451.0647109  17.005   9.361  25.757   8.464
        *NEW* (Placed in 13)                                    Known (#4)
 Unconnected minimum 13 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 13 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     17284.    
 decide> The unconnected minima in the chain and their distances are:
    13       25.86     7 
 

 tryconnect> 245-iteration DNEB run for minima 7_S and 13_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0420 Dev= 0.12% S= 27.11 time= 13.27
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  28.55

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1326 steps. Energy=    -447.8979489       time=      14.17
 Minus side of path:                    1328 steps. Energy=    -448.9404302       time=      14.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8979489  1.0977         -446.8002010  2.1402         -448.9404302  27.148  25.877   6.722  32.433
        Known (#13)                                             Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -450.6031786  3.0977        -447.5054453  3.0319        -450.5373870  74.408  49.573   3.834  56.865
   9     -450.5373870  3.7411        -446.7963160  3.6604        -450.4566997   9.393   8.166  29.501   7.390
   6     -450.4566997 0.82351        -449.6331861 0.33785        -449.9710327  36.947  35.777   3.075  70.895
   4     -449.9710327  7.0844        -442.8866637  6.0538        -448.9404302  14.749  10.226  14.405  15.133
  12     -448.9404302  2.1402        -446.8002010  1.0977        -447.8979489  27.148  25.877   6.722  32.433
  11     -447.8979489  6.0894        -441.8085026  9.2562        -451.0647109  17.005   9.361  25.757   8.464
   2     -451.0647109  3.2763        -447.7883684  2.2166        -450.0049219   6.662   5.758  42.407   5.141

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

 Elapsed time=                              1393.38
 OPTIM> # of energy calls=                        156 time=           1.16 %=  0.1
 OPTIM> # of energy+gradient calls=             88439 time=         666.63 %= 47.8
 OPTIM> # of energy+gradient+Hessian calls=      1166 time=         341.69 %= 24.5
