
 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 05/25/2012 at 12:49:20
  [-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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -445.9489550     RMS force=    0.9737620693E-06
 OPTIM> Final energy  =    -448.6696394     RMS force=    0.9290985868E-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=     43278.    
 decide> The unconnected minima in the chain and their distances are:
     2       35.11     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1629 Dev= 0.56% S= 36.50 time= 26.57
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=  50.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1260 steps. Energy=    -447.5826404       time=      13.96
 Minus side of path:                    1275 steps. Energy=    -448.6817042       time=      14.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5826404 0.24789         -447.3347538  1.3470         -448.6817042  19.514  19.133   3.017  72.267
        *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=     37587.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.48     3     3       33.24     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1240 Dev= 0.05% S= 9.52 time= 1.11
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  23.00

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1232 steps. Energy=    -447.5826404       time=      12.97
 Minus side of path:                    1379 steps. Energy=    -449.0495841       time=      17.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5826404 0.21447         -447.3681735  1.6814         -449.0495841  18.781  16.940   2.262  96.354
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 3_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0238 Dev= 0.51% S= 33.91 time= 21.85
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  67.18

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1301 steps. Energy=    -446.0663245       time=      16.75
 Minus side of path:                    1317 steps. Energy=    -447.5826404       time=      18.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0663245 0.17661         -445.8897105  1.6929         -447.5826404  33.459  31.683   2.187  99.695
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     6401.4    
 decide> The unconnected minima in the chain and their distances are:
     2        9.48     3     6       16.75     1 
 

 tryconnect> 735-iteration DNEB run for minima 2_F and 3_U using 21 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 735 RMS= 0.0086 Dev= 4.09% S= 10.81 time= 118.30
 Following    1 images are candidates for TS:   16  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=  22.07
 isnewts> transition state is the same as number        2 energy=     -447.3681734553
 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:                    1227 steps. Energy=    -447.5826404       time=      13.50
 Minus side of path:                    1376 steps. Energy=    -449.0495841       time=      15.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5826404 0.21447         -447.3681735  1.6814         -449.0495841  18.780  16.940   2.263  96.327
        Known (#3)                                              Known (#5)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0845 Dev= 0.02% S= 16.80 time= 6.64
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  30.43

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1315 steps. Energy=    -446.0663245       time=      13.70
 Minus side of path:                    1230 steps. Energy=    -445.9489550       time=      12.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0663245 0.13918         -445.9271453 0.21810E-01     -445.9489550  17.460  16.752   1.893 115.159
        Known (#6)                                              Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2552.0    
 decide> The unconnected minima in the chain and their distances are:
     2        9.48     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #3)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0077 Dev= 5.00% S= 10.91 time= 139.24
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  20.10
 isnewts> transition state is the same as number        2 energy=     -447.3681734555
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     5025.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.13     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0161 Dev= 0.06% S= 17.18 time= 6.65
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=  40.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1247 steps. Energy=    -448.6696394       time=      12.73
 Minus side of path:                    1312 steps. Energy=    -449.0495841       time=      13.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6696394 0.69010E-04     -448.6695704 0.38001         -449.0495841  17.222  17.132   2.833  76.945
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -445.9489550 0.21810E-01    -445.9271453 0.13918        -446.0663245  17.460  16.752   1.893 115.159
   3     -446.0663245 0.17661        -445.8897105  1.6929        -447.5826404  33.459  31.683   2.187  99.695
   2     -447.5826404 0.21447        -447.3681735  1.6814        -449.0495841  18.781  16.940   2.262  96.354
   6     -449.0495841 0.38001        -448.6695704 0.69010E-04    -448.6696394  17.222  17.132   2.833  76.945

 Number of TS in the path       =      4
 Number of cycles               =      5

 Elapsed time=                               749.50
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             67350 time=         503.93 %= 67.2
 OPTIM> # of energy+gradient+Hessian calls=       329 time=          97.59 %= 13.0
