
 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 05/24/2012 at 10:04:08
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    17
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>  321 Cartesian coordinates will be optimised for  107 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 =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -534.9554512     RMS force=    0.9785421381E-06
 OPTIM> Final energy  =    -535.5404266     RMS force=    0.8451572902E-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=     4196.1    
 decide> The unconnected minima in the chain and their distances are:
     2       16.13     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4701 Dev= 0.53% S= 19.90 time= 1.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.53

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     639 steps. Energy=    -534.4260049       time=       1.57
 Minus side of path:                     641 steps. Energy=    -535.4310466       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4260049  4.9684         -529.4576278  5.9734         -535.4310466  12.679  11.342   2.956  36.201
        *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      3 steps with      2 missing connections, weight=     2603.7    
 decide> The unconnected minima in the chain and their distances are:
     2       12.52     4     3        8.63     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 3.7889 Dev= 1.77% S= 14.65 time= 0.74
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   7.92

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     688 steps. Energy=    -535.4310466       time=       1.71
 Minus side of path:                     582 steps. Energy=    -535.0660358       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4310466 0.36506         -535.0659872 0.48656E-04     -535.0660358   3.873   3.787  31.064   3.445
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5592 Dev= 0.82% S= 9.66 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   4.01

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     644 steps. Energy=    -534.9554512       time=       1.60
 Minus side of path:                     637 steps. Energy=    -534.4260049       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.9554512  3.6055         -531.3499435  3.0761         -534.4260049  14.877   8.662  17.314   6.180
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1860.2    
 decide> The unconnected minima in the chain and their distances are:
     2       12.30     5 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.2461 Dev= 0.26% S= 13.73 time= 0.73
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.74

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     700 steps. Energy=    -536.9828464       time=       1.81
 Minus side of path:                     619 steps. Energy=    -535.4681083       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.9828464  4.5621         -532.4207949  3.0473         -535.4681083  12.312   9.186  16.483   6.492
        *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      5 steps with      2 missing connections, weight=     346.68    
 decide> The unconnected minima in the chain and their distances are:
     2        3.06     7     6        6.83     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      13.40095641    
 Double-ended search iterations= 70 RMS= 0.6022 Dev= 2.80% S= 3.64 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.89

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     632 steps. Energy=    -535.5404266       time=       1.57
 Minus side of path:                     596 steps. Energy=    -535.5989304       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.5404266 0.77489         -534.7655356 0.83339         -535.5989304  14.082  12.620   4.254  25.155
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3565 Dev= 0.26% S= 7.45 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.40

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     621 steps. Energy=    -536.9828464       time=       1.53
 Minus side of path:                     623 steps. Energy=    -535.4310466       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.9828464  3.8815         -533.1013267  2.3297         -535.4310466   9.390   6.851  10.393  10.295
        Known (#6)                                              Known (#4)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     57.291    
 decide> The unconnected minima in the chain and their distances are:
     2        3.06     7 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 7_S using 7 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.1122 Dev= 3.62% S= 4.64 time= 3.57
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   2.09

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     595 steps. Energy=    -535.4681083       time=       1.45
 Minus side of path:                     580 steps. Energy=    -535.5404266       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4681083  8.4373         -527.0308068  8.5096         -535.5404266   3.720   3.060  31.486   3.398
        Known (#7)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -534.9554512  3.6055        -531.3499435  3.0761        -534.4260049  14.877   8.662  17.314   6.180
   1     -534.4260049  4.9684        -529.4576278  5.9734        -535.4310466  12.679  11.342   2.956  36.201
   6     -535.4310466  2.3297        -533.1013267  3.8815        -536.9828464   9.390   6.851  10.393  10.295
   4     -536.9828464  4.5621        -532.4207949  3.0473        -535.4681083  12.312   9.186  16.483   6.492
   7     -535.4681083  8.4373        -527.0308068  8.5096        -535.5404266   3.720   3.060  31.486   3.398

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

 Elapsed time=                                61.35
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             16931 time=          34.51 %= 56.3
 OPTIM> # of energy+gradient+Hessian calls=       256 time=          13.85 %= 22.6
