
 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 09:37:16
  [-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=    -535.9257730     RMS force=    0.8587514276E-06
 OPTIM> Final energy  =    -534.7931080     RMS force=    0.9947334002E-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=     5414.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.56     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= 0.2272 Dev= 0.28% S= 19.05 time= 1.85
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.87

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     640 steps. Energy=    -535.9257730       time=       1.98
 Minus side of path:                     620 steps. Energy=    -534.1043783       time=       1.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.9257730  2.6980         -533.2277373 0.87664         -534.1043783  14.736  13.900   2.144  49.906
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1277.9    
 decide> The unconnected minima in the chain and their distances are:
     2       10.85     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.9956 Dev= 0.11% S= 11.67 time= 0.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        121
 DNEB run yielded 1 true transition state(s) time=  12.75

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     670 steps. Energy=    -535.0498216       time=       1.90
 Minus side of path:                     805 steps. Energy=    -534.1148070       time=       2.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.0498216  2.1890         -532.8608541  1.2540         -534.1148070  30.834  28.676   2.000  53.510
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     2278.6    
 decide> The unconnected minima in the chain and their distances are:
     2        9.22     5     4       11.43     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= 0.2186 Dev= 0.03% S= 9.30 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   8.07

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     609 steps. Energy=    -534.4788870       time=       1.49
 Minus side of path:                     571 steps. Energy=    -535.1145759       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4788870 0.33740         -534.1414823 0.97309         -535.1145759   7.449   6.251   9.433  11.343
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 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= 0.2337 Dev= 0.10% S= 12.02 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   7.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     620 steps. Energy=    -535.9257730       time=       1.84
 Minus side of path:                     695 steps. Energy=    -535.8189449       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.9257730 0.95420         -534.9715756 0.84737         -535.8189449   9.373   5.165  10.650  10.047
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1086.8    
 decide> The unconnected minima in the chain and their distances are:
     2        6.42     7     7        9.37     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 2.3084 Dev= 0.71% S= 6.67 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   4.06

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     548 steps. Energy=    -535.1145759       time=       1.34
 Minus side of path:                     547 steps. Energy=    -535.1720621       time=       1.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1145759 0.25710         -534.8574758 0.31459         -535.1720621   4.713   4.591   4.488  23.842
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.6535 Dev= 0.77% S= 10.01 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   5.24

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     600 steps. Energy=    -534.2564197       time=       1.76
 Minus side of path:                     610 steps. Energy=    -534.1043783       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.2564197 0.29918         -533.9572427 0.14714         -534.1043783   5.162   4.698  11.372   9.409
        *NEW* (Placed in 10)                                    Known (#3)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     447.43    
 decide> The unconnected minima in the chain and their distances are:
     2        4.28     9     7        7.17    10 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1205 Dev= 0.10% S= 4.46 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.20

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     544 steps. Energy=    -534.7931080       time=       1.31
 Minus side of path:                     565 steps. Energy=    -535.1720621       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7931080 0.23954E-01     -534.7691538 0.40291         -535.1720621   4.422   4.276  18.664   5.733
        Known (#2)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 4.9770 Dev= 0.42% S= 7.76 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        122
 DNEB run yielded 1 true transition state(s) time=  13.52

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     732 steps. Energy=    -534.1043783       time=       1.95
 Minus side of path:                     641 steps. Energy=    -534.2459137       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1043783 0.73024         -533.3741357 0.87178         -534.2459137  15.497  13.977   3.053  35.051
        Known (#3)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     712.53    
 decide> The unconnected minima in the chain and their distances are:
     6        8.88     5     5        2.23    11 
 

 tryconnect> 70-iteration DNEB run for minima 5_U and 6_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1119 Dev= 0.01% S= 8.90 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.45

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     603 steps. Energy=    -534.1148070       time=       1.47
 Minus side of path:                     659 steps. Energy=    -534.4788870       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1148070 0.40459E-01     -534.0743483 0.40454         -534.4788870  10.423   8.891   1.882  56.851
        Known (#5)                                              Known (#6)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 5_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2606 Dev= 1.43% S= 2.79 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.45

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     628 steps. Energy=    -534.2459137       time=       1.58
 Minus side of path:                     649 steps. Energy=    -534.1148070       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.2459137  8.5014         -525.7444754  8.3703         -534.1148070   3.118   2.235  44.877   2.384
        Known (#11)                                             Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -535.9257730  2.6980        -533.2277373 0.87664        -534.1043783  14.736  13.900   2.144  49.906
   8     -534.1043783 0.73024        -533.3741357 0.87178        -534.2459137  15.497  13.977   3.053  35.051
  10     -534.2459137  8.5014        -525.7444754  8.3703        -534.1148070   3.118   2.235  44.877   2.384
   9     -534.1148070 0.40459E-01    -534.0743483 0.40454        -534.4788870  10.423   8.891   1.882  56.851
   3     -534.4788870 0.33740        -534.1414823 0.97309        -535.1145759   7.449   6.251   9.433  11.343
   5     -535.1145759 0.25710        -534.8574758 0.31459        -535.1720621   4.713   4.591   4.488  23.842
   7     -535.1720621 0.40291        -534.7691538 0.23954E-01    -534.7931080   4.422   4.276  18.664   5.733

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

 Elapsed time=                               105.01
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             22403 time=          46.03 %= 43.8
 OPTIM> # of energy+gradient+Hessian calls=       543 time=          31.98 %= 30.5
