
 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 10:28:17
  [-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=    -539.2013737     RMS force=    0.9044628733E-06
 OPTIM> Final energy  =    -529.9086079     RMS force=    0.8739870662E-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=     49321.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.67     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 385 RMS= 0.1017 Dev= 0.71% S= 42.51 time= 8.39
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        192
 DNEB run yielded 1 true transition state(s) time=  20.20

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1050 steps. Energy=    -537.1836401       time=       2.94
 Minus side of path:                     901 steps. Energy=    -532.2096282       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.1836401  6.0668         -531.1168704  1.0928         -532.2096282  44.442  41.964   2.318  46.164
        *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=     3946.9    
 decide> The unconnected minima in the chain and their distances are:
     2       15.69     4     3        4.44     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.768894829    
 Double-ended search iterations= 140 RMS= 0.5952 Dev= 1.43% S= 18.69 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        119
 DNEB run yielded 1 true transition state(s) time=  11.70

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     835 steps. Energy=    -532.6882590       time=       2.36
 Minus side of path:                     660 steps. Energy=    -534.3665789       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6882590  2.3552         -530.3330421  4.0335         -534.3665789  30.525  28.182   3.956  27.045
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1370 Dev= 0.29% S= 4.60 time= 0.29
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.53

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     595 steps. Energy=    -539.2013737       time=       1.48
 Minus side of path:                     536 steps. Energy=    -537.1836401       time=       1.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -539.2013737  2.0396         -537.1617837 0.21856E-01     -537.1836401   5.186   4.445  12.375   8.647
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     5539.6    
 decide> The unconnected minima in the chain and their distances are:
     2       17.34     5     5        6.89     4 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 175 RMS= 0.3812 Dev= 0.50% S= 20.63 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   5.73

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1120 steps. Energy=    -532.4932861       time=       3.51
 Minus side of path:                     649 steps. Energy=    -532.1408339       time=       1.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4932861  4.1899         -528.3034159  3.8374         -532.1408339  25.611  16.435   2.706  39.539
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0664 Dev= 0.02% S= 6.91 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.06

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     620 steps. Energy=    -532.6882590       time=       1.53
 Minus side of path:                     627 steps. Energy=    -532.2096282       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.6882590 0.63487         -532.0533865 0.15624         -532.2096282   7.305   6.889   4.389  24.379
        Known (#5)                                              Known (#4)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     2804.8    
 decide> The unconnected minima in the chain and their distances are:
     2        9.98     8     8       12.19     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.3720 Dev= 0.33% S= 10.51 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.38
 isnewts> transition state is the same as number        4 energy=     -528.3034159056
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1105 steps. Energy=    -532.4932861       time=       3.57
 Minus side of path:                     648 steps. Energy=    -532.1408339       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4932861  4.1899         -528.3034159  3.8374         -532.1408339  25.618  16.455   2.670  40.069
        Known (#7)                                              Known (#8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 1.1832 Dev= 1.86% S= 16.95 time= 0.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        143
 DNEB run yielded 1 true transition state(s) time=  13.34

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     621 steps. Energy=    -532.1063474       time=       1.54
 Minus side of path:                     639 steps. Energy=    -532.2433104       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1063474 0.14872         -531.9576231 0.28569         -532.2433104  12.006  11.944   3.021  35.415
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     3671.3    
 decide> The unconnected minima in the chain and their distances are:
     2       11.20     7     8        9.86     9     9       10.94     4 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1170 Dev= 0.07% S= 11.38 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.07

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     634 steps. Energy=    -532.4932861       time=       1.59
 Minus side of path:                     612 steps. Energy=    -529.9086079       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4932861  2.9244         -529.5688947 0.33971         -529.9086079  13.057  11.239   4.647  23.023
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2063 Dev= 0.00% S= 9.89 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.19

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     622 steps. Energy=    -532.1408339       time=       1.55
 Minus side of path:                     641 steps. Energy=    -532.1063474       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1408339 0.81821         -531.3226195 0.78373         -532.1063474  10.351   9.860   3.644  29.367
        Known (#8)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 4_S and 9_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 1.4993 Dev= 1.23% S= 15.88 time= 0.58
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.46

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     628 steps. Energy=    -532.1408339       time=       1.55
 Minus side of path:                     670 steps. Energy=    -532.6882590       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.1408339  5.3895         -526.7513206  5.9369         -532.6882590  18.960  13.393   8.413  12.719
        Known (#8)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -539.2013737  2.0396        -537.1617837 0.21856E-01    -537.1836401   5.186   4.445  12.375   8.647
   1     -537.1836401  6.0668        -531.1168704  1.0928        -532.2096282  44.442  41.964   2.318  46.164
   5     -532.2096282 0.15624        -532.0533865 0.63487        -532.6882590   7.305   6.889   4.389  24.379
  10     -532.6882590  5.9369        -526.7513206  5.3895        -532.1408339  18.960  13.393   8.413  12.719
   4     -532.1408339  3.8374        -528.3034159  4.1899        -532.4932861  25.611  16.435   2.706  39.539
   8     -532.4932861  2.9244        -529.5688947 0.33971        -529.9086079  13.057  11.239   4.647  23.023

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                               126.76
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             29809 time=          59.83 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       680 time=          36.93 %= 29.1
