
 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 09:33:36
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.4269059     RMS force=    0.9672288491E-06
 OPTIM> Final energy  =    -534.9485339     RMS force=    0.9802420858E-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=     28066.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.39     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 315 RMS= 0.2391 Dev= 2.79% S= 36.41 time= 5.69
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     635 steps. Energy=    -532.5720133       time=       1.57
 Minus side of path:                     631 steps. Energy=    -534.9265980       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5720133  4.1775         -528.3944868  6.5321         -534.9265980   8.077   6.509  24.058   4.448
        *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=     45353.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.67     4     3       15.43     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.7245 Dev= 1.53% S= 38.42 time= 7.00
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=   7.31

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     931 steps. Energy=    -534.7157027       time=       2.48
 Minus side of path:                    1080 steps. Energy=    -534.9265980       time=       3.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7157027  2.7935         -531.9221663  3.0044         -534.9265980  34.949  30.478   2.622  40.809
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1227 Dev= 0.45% S= 16.41 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.69

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     866 steps. Energy=    -535.3831556       time=       2.28
 Minus side of path:                     631 steps. Energy=    -532.5137101       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3831556  3.2430         -532.1401994 0.37351         -532.5137101  24.914  23.919   2.366  45.229
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      3 missing connections, weight=     3827.6    
 decide> The unconnected minima in the chain and their distances are:
     2       10.46     5     4       13.79     6     7        3.93     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2260 Dev= 0.07% S= 10.53 time= 0.64
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.00

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     646 steps. Energy=    -534.7157027       time=       1.78
 Minus side of path:                     660 steps. Energy=    -534.9485339       time=       1.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7157027 0.25330         -534.4624059 0.48613         -534.9485339  10.770  10.459   2.580  41.470
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 4_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 2.7633 Dev= 1.57% S= 15.87 time= 1.12
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     667 steps. Energy=    -535.3831556       time=       1.69
 Minus side of path:                     645 steps. Energy=    -533.4547457       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3831556  3.4087         -531.9744810  1.4803         -533.4547457  13.479   5.023  25.120   4.260
        Known (#6)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0550 Dev= 0.08% S= 3.96 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.68

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     600 steps. Energy=    -532.5137101       time=       1.54
 Minus side of path:                     624 steps. Energy=    -533.4269059       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5137101 0.31339E-01     -532.4823712 0.94453         -533.4269059   4.042   3.933  10.163  10.529
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1888.1    
 decide> The unconnected minima in the chain and their distances are:
     4       12.36     8 
 

 tryconnect> 105-iteration DNEB run for minima 4_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1627 Dev= 0.17% S= 12.90 time= 0.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.09

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     830 steps. Energy=    -533.4479457       time=       2.45
 Minus side of path:                     641 steps. Energy=    -534.9265980       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4479457 0.56314         -532.8848076  2.0418         -534.9265980  12.238   9.182   3.016  35.483
        *NEW* (Placed in 9)                                     Known (#4)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     87.862    
 decide> The unconnected minima in the chain and their distances are:
     9        4.45     8 
 

 tryconnect> 70-iteration DNEB run for minima 8_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.4023 Dev= 0.01% S= 4.45 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.56

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     637 steps. Energy=    -533.4479457       time=       1.59
 Minus side of path:                     653 steps. Energy=    -533.4547457       time=       1.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4479457 0.33934E-03     -533.4476064 0.71393E-02     -533.4547457   4.470   4.445   2.447  43.719
        Known (#9)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -533.4269059 0.94453        -532.4823712 0.31339E-01    -532.5137101   4.042   3.933  10.163  10.529
   3     -532.5137101 0.37351        -532.1401994  3.2430        -535.3831556  24.914  23.919   2.366  45.229
   5     -535.3831556  3.4087        -531.9744810  1.4803        -533.4547457  13.479   5.023  25.120   4.260
   8     -533.4547457 0.71393E-02    -533.4476064 0.33934E-03    -533.4479457   4.470   4.445   2.447  43.719
   7     -533.4479457 0.56314        -532.8848076  2.0418        -534.9265980  12.238   9.182   3.016  35.483
   2     -534.9265980  3.0044        -531.9221663  2.7935        -534.7157027  34.949  30.478   2.622  40.809
   4     -534.7157027 0.25330        -534.4624059 0.48613        -534.9485339  10.770  10.459   2.580  41.470

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                                82.81
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             25688 time=          51.26 %= 61.9
 OPTIM> # of energy+gradient+Hessian calls=       278 time=          15.09 %= 18.2
