
 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 21:45:59
  [-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=    -448.4008918     RMS force=    0.8469745680E-06
 OPTIM> Final energy  =    -460.8048640     RMS force=    0.8370556211E-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=    0.85708E+06
 decide> The unconnected minima in the chain and their distances are:
     2       94.99     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      697.3792467    
 Double-ended search iterations= 1080 RMS= 1.4497 Dev= 0.09% S= 103.15 time= 186.56
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        139
 DNEB run yielded 1 true transition state(s) time=  80.70

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    2044 steps. Energy=    -460.8048640       time=      28.96
 Minus side of path:                    1668 steps. Energy=    -452.9138167       time=      20.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.8048640  12.270         -448.5349722  4.3788         -452.9138167  85.246  69.523   2.112 103.200
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.35801E+06
 decide> The unconnected minima in the chain and their distances are:
     3       71.01     1 
 

 tryconnect> 735-iteration DNEB run for minima 1_S and 3_F using 21 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 735 RMS= 0.2124 Dev= 0.23% S= 74.10 time= 116.03
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        176
 DNEB run yielded 1 true transition state(s) time=  98.55

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1678 steps. Energy=    -452.9138167       time=      27.33
 Minus side of path:                    1600 steps. Energy=    -451.7743280       time=      22.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9138167  5.7993         -447.1145030  4.6598         -451.7743280  58.563  43.850   1.946 112.021
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.50489E+06
 decide> The unconnected minima in the chain and their distances are:
     4       79.63     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 4_F using 23 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.7984714498E-01
 Double-ended search iterations= 805 RMS= 0.0285 Dev= 8.35% S= 102.48 time= 140.03
 Following    2 images are candidates for TS:   11   19  
 Converged to TS (number of iterations):         76
 Converged to TS (number of iterations):         24
 DNEB run yielded 2 true transition state(s) time=  70.15

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1703 steps. Energy=    -452.9138167       time=      25.54
 Minus side of path:                    1514 steps. Energy=    -449.2479958       time=      20.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9138167  6.9798         -445.9339711  3.3140         -449.2479958  71.522  60.330   1.498 145.568
        Known (#3)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1259 steps. Energy=    -448.3177435       time=      15.25
 Minus side of path:                    1333 steps. Energy=    -451.7743280       time=      15.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3177435 0.10716         -448.2105859  3.5637         -451.7743280  29.862  27.002   4.042  53.931
        *NEW* (Placed in 6)                                     Known (#4)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.14846E+06
 decide> The unconnected minima in the chain and their distances are:
     5       52.95     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 5_F using 15 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0483 Dev= 0.98% S= 57.95 time= 60.03
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  31.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1330 steps. Energy=    -448.4008918       time=      15.09
 Minus side of path:                    1617 steps. Energy=    -449.2479958       time=      22.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4008918 0.46874         -447.9321512  1.3158         -449.2479958  55.757  53.211   3.870  56.325
        Known (#1)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -448.4008918 0.46874        -447.9321512  1.3158        -449.2479958  55.757  53.211   3.870  56.325
   3     -449.2479958  3.3140        -445.9339711  6.9798        -452.9138167  71.522  60.330   1.498 145.568
   1     -452.9138167  4.3788        -448.5349722  12.270        -460.8048640  85.246  69.523   2.112 103.200

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                               997.25
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             89386 time=         666.88 %= 66.9
 OPTIM> # of energy+gradient+Hessian calls=       450 time=         134.38 %= 13.5
