
 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 10:00:41
  [-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=    -530.5852566     RMS force=    0.9815690227E-06
 OPTIM> Final energy  =    -532.6759545     RMS force=    0.9129916502E-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=     8233.5    
 decide> The unconnected minima in the chain and their distances are:
     2       20.19     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.5170 Dev= 0.51% S= 28.38 time= 2.66
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=   5.32

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     610 steps. Energy=    -532.5296150       time=       1.53
 Minus side of path:                     570 steps. Energy=    -532.1388609       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.5296150 0.43944         -532.0901701 0.48691E-01     -532.1388609   2.950   2.736  24.582   4.353
        *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=     6770.4    
 decide> The unconnected minima in the chain and their distances are:
     2       12.09     3     4       17.10     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4708 Dev= 0.43% S= 16.90 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     641 steps. Energy=    -533.2800415       time=       1.62
 Minus side of path:                     699 steps. Energy=    -533.7331057       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2800415  4.3555         -528.9245116  4.8086         -533.7331057  19.322  10.914  12.491   8.566
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2534 Dev= 1.68% S= 19.73 time= 1.88
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         45
 Converged to TS (number of iterations):        117
 DNEB run yielded 2 true transition state(s) time=  15.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     610 steps. Energy=    -532.1323945       time=       1.52
 Minus side of path:                     756 steps. Energy=    -533.2800415       time=       1.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1323945  2.6262         -529.5061666  3.7739         -533.2800415  18.194  16.320   4.929  21.710
        *NEW* (Placed in 7)                                     Known (#5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     665 steps. Energy=    -532.6759545       time=       1.69
 Minus side of path:                     626 steps. Energy=    -532.6759545       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6759545  1.1538         -531.5221110  1.1538         -532.6759545   8.447   3.144  50.432   2.122
        *NEW* (Placed in 8)                                     Known (#8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     470.98    
 decide> The unconnected minima in the chain and their distances are:
     2        5.58     6     7        6.67     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.2690 Dev= 1.54% S= 6.13 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     580 steps. Energy=    -532.6759545       time=       1.44
 Minus side of path:                     591 steps. Energy=    -533.2800415       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6759545 0.36830E-01     -532.6391244 0.64092         -533.2800415   2.828   2.715  34.154   3.133
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F 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= 0.1722 Dev= 0.14% S= 6.80 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   2.91

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     598 steps. Energy=    -530.5852566       time=       1.49
 Minus side of path:                     704 steps. Energy=    -532.1323945       time=       2.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566 0.30820         -530.2770606  1.8553         -532.1323945   7.677   6.674   4.046  26.446
        Known (#1)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     92.360    
 decide> The unconnected minima in the chain and their distances are:
     9        4.52     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.5936 Dev= 0.81% S= 5.04 time= 0.41
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  26.78
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     184.72    
 decide> The unconnected minima in the chain and their distances are:
     9        4.52     6 
 

 tryconnect> 350-iteration DNEB run for minima 6_S and 9_F using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 350 RMS= 0.0887 Dev= 19.06% S= 6.75 time= 7.14
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.38

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     613 steps. Energy=    -533.2800415       time=       1.51
 Minus side of path:                     600 steps. Energy=    -533.7331057       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2800415  8.2885         -524.9915332  8.7416         -533.7331057   5.571   4.520   6.006  17.816
        Known (#9)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -530.5852566 0.30820        -530.2770606  1.8553        -532.1323945   7.677   6.674   4.046  26.446
   3     -532.1323945  2.6262        -529.5061666  3.7739        -533.2800415  18.194  16.320   4.929  21.710
   2     -533.2800415  4.3555        -528.9245116  4.8086        -533.7331057  19.322  10.914  12.491   8.566
   7     -533.7331057  8.7416        -524.9915332  8.2885        -533.2800415   5.571   4.520   6.006  17.816
   5     -533.2800415 0.64092        -532.6391244 0.36830E-01    -532.6759545   2.828   2.715  34.154   3.133

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

 Elapsed time=                                97.89
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21528 time=          43.54 %= 44.5
 OPTIM> # of energy+gradient+Hessian calls=       549 time=          31.59 %= 32.3
