
 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 11:45:53
  [-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=    -532.2091826     RMS force=    0.9513600595E-06
 OPTIM> Final energy  =    -529.6058042     RMS force=    0.9327745603E-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=     5746.9    
 decide> The unconnected minima in the chain and their distances are:
     2       17.91     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.5129 Dev= 0.37% S= 24.83 time= 1.95
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     587 steps. Energy=    -532.2091826       time=       1.45
 Minus side of path:                     636 steps. Energy=    -533.1879325       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2091826 0.27916         -531.9300185  1.2579         -533.1879325   5.701   5.502  10.340  10.348
        *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=     4217.6    
 decide> The unconnected minima in the chain and their distances are:
     2       14.80     4     3        9.91     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.4960 Dev= 0.17% S= 15.49 time= 1.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.32

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     855 steps. Energy=    -533.1879325       time=       2.24
 Minus side of path:                     647 steps. Energy=    -529.6058042       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1879325  4.4926         -528.6953752 0.91043         -529.6058042  17.161  14.832   5.752  18.602
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.2227 Dev= 1.21% S= 15.16 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.73

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     813 steps. Energy=    -531.0120926       time=       2.11
 Minus side of path:                     626 steps. Energy=    -532.4532641       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0120926  1.7903         -529.2217993  3.2315         -532.4532641  18.711  10.858  16.269   6.577
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     435.60    
 decide> The unconnected minima in the chain and their distances are:
     3        4.35     6     5        7.07     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.1969 Dev= 0.14% S= 4.44 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.20

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     590 steps. Energy=    -532.4532641       time=       1.44
 Minus side of path:                     582 steps. Energy=    -532.2091826       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641 0.26250         -532.1907646 0.18418E-01     -532.2091826   4.544   4.352  14.598   7.330
        Known (#6)                                              Known (#3)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4203 Dev= 0.46% S= 7.47 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.19

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     595 steps. Energy=    -531.2468759       time=       1.45
 Minus side of path:                     590 steps. Energy=    -531.0120926       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.2468759 0.52149         -530.7253829 0.28671         -531.0120926   4.741   4.262   8.991  11.900
        *NEW* (Placed in 7)                                     Known (#5)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     169.32    
 decide> The unconnected minima in the chain and their distances are:
     7        5.53     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 5.1592 Dev= 1.19% S= 6.07 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.91

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     598 steps. Energy=    -532.4532641       time=       1.47
 Minus side of path:                     587 steps. Energy=    -532.2091826       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641 0.26250         -532.1907646 0.18418E-01     -532.2091826   4.544   4.352  14.599   7.329
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     88.324    
 decide> The unconnected minima in the chain and their distances are:
     5        4.45     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2984 Dev= 0.86% S= 5.03 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=   7.90

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     604 steps. Energy=    -531.8544326       time=       1.48
 Minus side of path:                     637 steps. Energy=    -531.0120926       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8544326  1.0933         -530.7610929 0.25100         -531.0120926  12.480  10.736   5.972  17.916
        *NEW* (Placed in 9)                                     Known (#5)
 Unconnected minimum 9 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     92.248    
 decide> The unconnected minima in the chain and their distances are:
     9        4.52     1 
 

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.4290 Dev= 0.60% S= 5.07 time= 0.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   4.79

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     609 steps. Energy=    -531.2468759       time=       1.50
 Minus side of path:                     629 steps. Energy=    -531.8544326       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.2468759 0.53874         -530.7081347  1.1463         -531.8544326   9.665   8.647   6.058  17.664
        Known (#7)                                              Known (#9)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     94.546    
 decide> The unconnected minima in the chain and their distances are:
     7        4.56     8 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.3729 Dev= 1.59% S= 5.17 time= 0.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.61
 isnewts> transition state is the same as number        5 energy=     -530.7253828971
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     614 steps. Energy=    -531.0120926       time=       1.52
 Minus side of path:                     596 steps. Energy=    -531.2468759       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0120926 0.28671         -530.7253829 0.52149         -531.2468759   4.741   4.262   8.992  11.900
        Known (#5)                                              Known (#7)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 9 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     176.65    
 decide> The unconnected minima in the chain and their distances are:
     5        4.45     8 
 

 tryconnect> 350-iteration DNEB run for minima 5_F and 8_S using 10 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      17.95856326    
 Double-ended search iterations= 350 RMS= 0.1476 Dev= 7.31% S= 5.84 time= 7.19
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.27

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     562 steps. Energy=    -532.4532641       time=       1.36
 Minus side of path:                     668 steps. Energy=    -531.0120926       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4532641  8.9988         -523.4544720  7.5576         -531.0120926   6.360   4.454   6.945  15.407
        Known (#8)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -532.2091826 0.18418E-01    -532.1907646 0.26250        -532.4532641   4.544   4.352  14.599   7.329
  10     -532.4532641  8.9988        -523.4544720  7.5576        -531.0120926   6.360   4.454   6.945  15.407
   3     -531.0120926  1.7903        -529.2217993  3.2315        -532.4532641  18.711  10.858  16.269   6.577
   4     -532.4532641 0.26250        -532.1907646 0.18418E-01    -532.2091826   4.544   4.352  14.598   7.330
   1     -532.2091826 0.27916        -531.9300185  1.2579        -533.1879325   5.701   5.502  10.340  10.348
   2     -533.1879325  4.4926        -528.6953752 0.91043        -529.6058042  17.161  14.832   5.752  18.602

 Number of TS in the path       =      6
 Number of cycles               =      8

 Elapsed time=                                92.55
 OPTIM> # of energy calls=                         66 time=           0.13 %=  0.1
 OPTIM> # of energy+gradient calls=             25099 time=          50.31 %= 54.4
 OPTIM> # of energy+gradient+Hessian calls=       419 time=          22.73 %= 24.6
