
 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 11:40:06
  [-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.
 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=    -530.5852566     RMS force=    0.9815690227E-06
 OPTIM> Final energy  =    -529.8722765     RMS force=    0.9707534666E-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=     2540.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.64     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= 0.3833 Dev= 1.26% S= 19.11 time= 1.25
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   7.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     603 steps. Energy=    -532.4532641       time=       1.51
 Minus side of path:                     605 steps. Energy=    -533.2255430       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641  2.6934         -529.7598950  3.4656         -533.2255430   9.333   6.924   9.117  11.736
        *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=     1669.0    
 decide> The unconnected minima in the chain and their distances are:
     2        7.37     3     4       10.83     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.5819 Dev= 0.13% S= 8.15 time= 0.40
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   6.01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     616 steps. Energy=    -532.4532641       time=       1.67
 Minus side of path:                     577 steps. Energy=    -530.2320384       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641  2.2709         -530.1823776 0.49661E-01     -530.2320384   5.780   4.122  23.081   4.636
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.7428 Dev= 0.62% S= 16.52 time= 0.78
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     601 steps. Energy=    -530.5852566       time=       1.52
 Minus side of path:                     619 steps. Energy=    -533.2255430       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566 0.59228E-01     -530.5260290  2.6995         -533.2255430   6.553   4.373  22.314   4.795
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1148.8    
 decide> The unconnected minima in the chain and their distances are:
     2        5.59     5     4        9.91     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1676 Dev= 0.08% S= 5.78 time= 0.40
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  27.80

 checkpair> Energies of the minima in the pair     4    6 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.8678 Dev= 0.29% S= 15.06 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     720 steps. Energy=    -532.1827447       time=       1.85
 Minus side of path:                     659 steps. Energy=    -533.2255430       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1827447  2.0185         -530.1642372  3.0613         -533.2255430  18.853  10.798  16.179   6.614
        *NEW* (Placed in 7)                                     Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     441.22    
 decide> The unconnected minima in the chain and their distances are:
     2        5.59     5     7        4.50     6 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 5_U using 12 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 420 RMS= 0.0162 Dev= 4.96% S= 6.95 time= 10.33
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     597 steps. Energy=    -530.1820588       time=       1.50
 Minus side of path:                     541 steps. Energy=    -529.8722765       time=       1.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1820588 0.31207         -529.8699912 0.22853E-02     -529.8722765   3.759   3.667  15.883   6.737
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 6_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 5.8022 Dev= 1.15% S= 5.29 time= 0.39
 Following    1 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   6.69

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     600 steps. Energy=    -532.1827447       time=       1.50
 Minus side of path:                     592 steps. Energy=    -532.1046118       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1827447 0.97479E-01     -532.0852658 0.19346E-01     -532.1046118   3.824   3.582  28.880   3.705
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     250.29    
 decide> The unconnected minima in the chain and their distances are:
     8        4.07     5     7        4.50     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1097 Dev= 0.16% S= 4.23 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.67

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     538 steps. Energy=    -530.1820588       time=       1.33
 Minus side of path:                     582 steps. Energy=    -530.2320384       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1820588 0.22917E-01     -530.1591413 0.72897E-01     -530.2320384   4.219   4.073  16.888   6.336
        Known (#8)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 6_S and 7_F using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 350 RMS= 0.0514 Dev= 6.74% S= 6.47 time= 7.19
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.42

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     629 steps. Energy=    -532.1827447       time=       1.58
 Minus side of path:                     581 steps. Energy=    -533.2255430       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1827447  7.9157         -524.2670609  8.9585         -533.2255430   6.277   4.504   7.115  15.038
        Known (#7)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -530.5852566 0.59228E-01    -530.5260290  2.6995        -533.2255430   6.553   4.373  22.314   4.795
   8     -533.2255430  8.9585        -524.2670609  7.9157        -532.1827447   6.277   4.504   7.115  15.038
   4     -532.1827447  2.0185        -530.1642372  3.0613        -533.2255430  18.853  10.798  16.179   6.614
   1     -533.2255430  3.4656        -529.7598950  2.6934        -532.4532641   9.333   6.924   9.117  11.736
   2     -532.4532641  2.2709        -530.1823776 0.49661E-01    -530.2320384   5.780   4.122  23.081   4.636
   7     -530.2320384 0.72897E-01    -530.1591413 0.22917E-01    -530.1820588   4.219   4.073  16.888   6.336
   5     -530.1820588 0.31207        -529.8699912 0.22853E-02    -529.8722765   3.759   3.667  15.883   6.737

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

 Elapsed time=                               111.35
 OPTIM> # of energy calls=                         78 time=           0.16 %=  0.1
 OPTIM> # of energy+gradient calls=             26971 time=          54.26 %= 48.7
 OPTIM> # of energy+gradient+Hessian calls=       556 time=          31.48 %= 28.3
