
 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 10:01:47
  [-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=    -523.5602712     RMS force=    0.8945014489E-06
 OPTIM> Final energy  =    -535.8471680     RMS force=    0.9673476979E-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=     67050.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.63     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 420 RMS= 0.3579 Dev= 2.02% S= 50.54 time= 10.07
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     635 steps. Energy=    -523.5602712       time=       1.56
 Minus side of path:                     636 steps. Energy=    -524.4763572       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -523.5602712 0.41724         -523.1430294  1.3333         -524.4763572   5.682   5.300  11.459   9.337
        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=     67181.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.65     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 3_S using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1197 Dev= 1.72% S= 53.46 time= 10.05
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=   5.39

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     648 steps. Energy=    -524.4763572       time=       1.69
 Minus side of path:                    1222 steps. Energy=    -530.9711214       time=       3.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -524.4763572  1.2089         -523.2674447  7.7037         -530.9711214  33.253  30.139   2.153  49.703
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     35607.    
 decide> The unconnected minima in the chain and their distances are:
     2       32.90     4 
 

 tryconnect> 315-iteration DNEB run for minima 2_F and 4_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.4613 Dev= 0.26% S= 37.93 time= 5.79
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   7.40

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     579 steps. Energy=    -534.4053048       time=       1.48
 Minus side of path:                     659 steps. Energy=    -535.3286702       time=       1.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4053048  1.0354         -533.3699188  1.9588         -535.3286702  18.746  17.041   4.670  22.913
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     11428.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.38     6     5       18.35     4 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1154 Dev= 0.22% S= 18.29 time= 1.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=   5.67

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     831 steps. Energy=    -537.3209327       time=       2.22
 Minus side of path:                     830 steps. Energy=    -535.8471680       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.3209327  3.7767         -533.5441957  2.3030         -535.8471680  21.145  14.827   4.539  23.574
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 4_S and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1765 Dev= 0.12% S= 18.83 time= 1.87
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.11

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     623 steps. Energy=    -530.9711214       time=       1.54
 Minus side of path:                     619 steps. Energy=    -531.2347856       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.9711214 0.32411E-01     -530.9387101 0.29608         -531.2347856   4.422   4.254  16.861   6.346
        Known (#4)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     8525.3    
 decide> The unconnected minima in the chain and their distances are:
     7       15.32     6     5       17.02     8 
 

 tryconnect> 140-iteration DNEB run for minima 6_U and 7_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1414 Dev= 0.08% S= 15.68 time= 1.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         85
 DNEB run yielded 1 true transition state(s) time=   8.01

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1071 steps. Energy=    -538.2240813       time=       3.23
 Minus side of path:                     647 steps. Energy=    -535.3286702       time=       1.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.2240813  2.9841         -535.2399693 0.88701E-01     -535.3286702  18.804  16.410   2.618  40.876
        *NEW* (Placed in 9)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 5_U and 8_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.2007 Dev= 0.10% S= 17.42 time= 1.87
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.63

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     595 steps. Energy=    -531.2347856       time=       1.45
 Minus side of path:                     658 steps. Energy=    -533.1340737       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.2347856 0.34952E-01     -531.1998335  1.9342         -533.1340737  14.191  13.985   2.896  36.943
        Known (#8)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     3923.0    
 decide> The unconnected minima in the chain and their distances are:
     7       15.03     9     5        8.08    10 
 

 tryconnect> 140-iteration DNEB run for minima 7_F and 9_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0632 Dev= 0.10% S= 15.26 time= 1.23
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.18

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     611 steps. Energy=    -537.3209327       time=       1.51
 Minus side of path:                     759 steps. Energy=    -538.2240813       time=       1.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.3209327 0.34779         -536.9731436  1.2509         -538.2240813  16.550  15.038   4.258  25.126
        Known (#7)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 5_F and 10_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6136 Dev= 0.03% S= 8.15 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=   3.10

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     594 steps. Energy=    -533.1340737       time=       1.46
 Minus side of path:                     613 steps. Energy=    -534.4053048       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1340737 0.25275         -532.8813212  1.5240         -534.4053048  11.634   8.094   1.829  58.499
        Known (#10)                                             Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -523.5602712 0.41724        -523.1430294  1.3333        -524.4763572   5.682   5.300  11.459   9.337
   2     -524.4763572  1.2089        -523.2674447  7.7037        -530.9711214  33.253  30.139   2.153  49.703
   5     -530.9711214 0.32411E-01    -530.9387101 0.29608        -531.2347856   4.422   4.254  16.861   6.346
   7     -531.2347856 0.34952E-01    -531.1998335  1.9342        -533.1340737  14.191  13.985   2.896  36.943
   9     -533.1340737 0.25275        -532.8813212  1.5240        -534.4053048  11.634   8.094   1.829  58.499
   3     -534.4053048  1.0354        -533.3699188  1.9588        -535.3286702  18.746  17.041   4.670  22.913
   6     -535.3286702 0.88701E-01    -535.2399693  2.9841        -538.2240813  18.804  16.410   2.618  40.876
   8     -538.2240813  1.2509        -536.9731436 0.34779        -537.3209327  16.550  15.038   4.258  25.126
   4     -537.3209327  3.7767        -533.5441957  2.3030        -535.8471680  21.145  14.827   4.539  23.574

 Number of TS in the path       =      9
 Number of cycles               =      6

 Elapsed time=                               118.10
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             35630 time=          71.00 %= 60.1
 OPTIM> # of energy+gradient+Hessian calls=       460 time=          24.80 %= 21.0
