
 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 10:42:05
  [-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=    -538.8653489     RMS force=    0.8788974546E-06
 OPTIM> Final energy  =    -532.8463297     RMS force=    0.9846727964E-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=     3386.6    
 decide> The unconnected minima in the chain and their distances are:
     2       15.02     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 0.7482 Dev= 1.19% S= 20.73 time= 1.17
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   5.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     636 steps. Energy=    -538.8653489       time=       1.58
 Minus side of path:                     632 steps. Energy=    -535.4681083       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8653489  8.7229         -530.1424797  5.3256         -535.4681083  10.987   9.036  12.206   8.766
        *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=     1245.8    
 decide> The unconnected minima in the chain and their distances are:
     2        6.48     4     3        9.91     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3607 Dev= 0.27% S= 6.70 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.50

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     583 steps. Energy=    -532.9691188       time=       1.54
 Minus side of path:                     689 steps. Energy=    -535.4681083       time=       1.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9691188 0.15998         -532.8091344  2.6590         -535.4681083   7.183   6.253   8.159  13.115
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U 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_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 5.6743 Dev= 2.37% S= 14.26 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.82

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     627 steps. Energy=    -538.7455757       time=       1.66
 Minus side of path:                     632 steps. Energy=    -538.8653489       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.7455757  8.4902         -530.2553443  8.6100         -538.8653489  10.366   9.913   3.684  29.048
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1953.3    
 decide> The unconnected minima in the chain and their distances are:
     2        1.69     5     3        9.91     1 
 

 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= 0.0204 Dev= 0.03% S= 1.70 time= 0.29
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.09

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     552 steps. Energy=    -532.9691188       time=       1.44
 Minus side of path:                     569 steps. Energy=    -532.8463297       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.9691188 0.12422         -532.8448981 0.14316E-02     -532.8463297   1.705   1.695  14.266   7.500
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

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

 tryconnect> 770-iteration DNEB run for minima 1_S and 3_F using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 770 RMS= 1.2073 Dev= 3.07% S= 21.74 time= 33.09
 Following    2 images are candidates for TS:   13   18  
 Converged to TS (number of iterations):         58
 Converged to TS (number of iterations):        166
 DNEB run yielded 2 true transition state(s) time=  22.58

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     645 steps. Energy=    -538.0726647       time=       1.59
 Minus side of path:                     650 steps. Energy=    -538.0678732       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0726647  2.7196         -535.3530426  2.7148         -538.0678732  16.362  10.164  15.445   6.928
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     595 steps. Energy=    -537.8077257       time=       1.45
 Minus side of path:                     613 steps. Energy=    -538.0726647       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.8077257 0.72254E-01     -537.7354714 0.33719         -538.0726647  12.346  12.196   6.562  16.307
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1574.9    
 decide> The unconnected minima in the chain and their distances are:
     3        5.57     9     9       11.19     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0949 Dev= 0.03% S= 5.60 time= 0.28
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=   6.25

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     585 steps. Energy=    -537.8077257       time=       1.42
 Minus side of path:                     644 steps. Energy=    -538.8653489       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.8077257 0.42769E-02     -537.8034488  1.0619         -538.8653489   5.653   5.574   4.081  26.221
        Known (#9)                                              Known (#3)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 105 RMS= 0.6548 Dev= 1.18% S= 15.70 time= 0.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   7.19

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     657 steps. Energy=    -538.0678732       time=       1.62
 Minus side of path:                     639 steps. Energy=    -538.0726647       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0678732  2.7148         -535.3530426  2.7196         -538.0726647  16.363  10.167  15.421   6.938
        *NEW* (Placed in 11)                                    Known (#10)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2411.1    
 decide> The unconnected minima in the chain and their distances are:
     4       13.41     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 4_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 6.0004 Dev= 3.01% S= 19.54 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.74
 isnewts> transition state is the same as number        1 energy=     -530.1424797040
 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:                     621 steps. Energy=    -538.8653489       time=       1.52
 Minus side of path:                     645 steps. Energy=    -535.4681083       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8653489  8.7229         -530.1424797  5.3256         -535.4681083  10.987   9.036  12.222   8.755
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2428.4    
 decide> The unconnected minima in the chain and their distances are:
     6       13.44     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 6_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.5238 Dev= 0.79% S= 18.19 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.37

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     686 steps. Energy=    -538.8653489       time=       1.71
 Minus side of path:                     712 steps. Energy=    -538.9350330       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.8653489  4.8518         -534.0135734  4.9215         -538.9350330  25.194  10.803  12.354   8.661
        Known (#1)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     53.215    
 decide> The unconnected minima in the chain and their distances are:
     3        3.76    12 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5328 Dev= 0.54% S= 4.55 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.32

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     580 steps. Energy=    -538.7455757       time=       1.41
 Minus side of path:                     615 steps. Energy=    -538.9350330       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.7455757 0.34668         -538.3988934 0.53614         -538.9350330  13.618  12.966   3.443  31.082
        Known (#6)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -538.8653489  4.8518        -534.0135734  4.9215        -538.9350330  25.194  10.803  12.354   8.661
  11     -538.9350330 0.53614        -538.3988934 0.34668        -538.7455757  13.618  12.966   3.443  31.082
   3     -538.7455757  8.4902        -530.2553443  8.6100        -538.8653489  10.366   9.913   3.684  29.048
   1     -538.8653489  8.7229        -530.1424797  5.3256        -535.4681083  10.987   9.036  12.206   8.766
   2     -535.4681083  2.6590        -532.8091344 0.15998        -532.9691188   7.183   6.253   8.159  13.115
   4     -532.9691188 0.12422        -532.8448981 0.14316E-02    -532.8463297   1.705   1.695  14.266   7.500

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               139.25
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41095 time=          82.19 %= 59.0
 OPTIM> # of energy+gradient+Hessian calls=       593 time=          31.90 %= 22.9
