
 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 05/25/2012 at 12:23:28
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
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>  654 Cartesian coordinates will be optimised for  218 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 =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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=    -450.1383146     RMS force=    0.9503218168E-06
 OPTIM> Final energy  =    -450.1554378     RMS force=    0.9581620243E-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=     54998.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.03     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0718 Dev= 1.37% S= 42.86 time= 34.76
 Following    3 images are candidates for TS:    3    8   10  
 Converged to TS (number of iterations):         76
 Converged to TS (number of iterations):         69
 Converged to TS (number of iterations):         30
 DNEB run yielded 3 true transition state(s) time= 147.07

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1432 steps. Energy=    -451.5125124       time=      17.87
 Minus side of path:                    1289 steps. Energy=    -450.1383146       time=      17.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5125124  1.9176         -449.5949093 0.54341         -450.1383146  56.440  52.337   2.272  95.934
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1485 steps. Energy=    -451.2817251       time=      21.67
 Minus side of path:                    1383 steps. Energy=    -452.4419066       time=      19.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.2817251 0.48319         -450.7985401  1.6434         -452.4419066  29.509  26.262   2.187  99.660
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1298 steps. Energy=    -450.1554378       time=      16.49
 Minus side of path:                    1307 steps. Energy=    -451.2817251       time=      16.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.1554378 0.18259         -449.9728513  1.3089         -451.2817251  11.362  10.975   3.187  68.408
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     47816.    
 decide> The unconnected minima in the chain and their distances are:
     4       36.30     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 4_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0392 Dev= 0.33% S= 39.42 time= 28.87
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=  46.21

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1957 steps. Energy=    -451.3336395       time=      31.89
 Minus side of path:                    1332 steps. Energy=    -450.1383146       time=      15.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.3336395  1.9673         -449.3663245 0.77199         -450.1383146  64.458  32.919   2.176 100.201
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     6187.2    
 decide> The unconnected minima in the chain and their distances are:
     2       18.36     6 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 6_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0892 Dev= 0.15% S= 19.12 time= 7.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=  35.26
 isnewts> transition state is the same as number        3 energy=     -449.9728512993
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1294 steps. Energy=    -450.1554378       time=      13.63
 Minus side of path:                    1303 steps. Energy=    -451.2817251       time=      13.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.1554378 0.18259         -449.9728513  1.3089         -451.2817251  11.362  10.975   3.187  68.406
        Known (#2)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     12374.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.36     6 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.0127 Dev= 6.10% S= 26.06 time= 147.84
 Following    2 images are candidates for TS:    2   11  
 Converged to TS (number of iterations):         17
 Converged to TS (number of iterations):         50
 DNEB run yielded 2 true transition state(s) time=  57.62
 isnewts> transition state is the same as number        3 energy=     -449.9728512993
 tryconnect> Will not repeat search for TS      1 same as TS      3
 isnewts> transition state is the same as number        2 energy=     -450.7985401317
 tryconnect> Try the path again for ts      2 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:                    1399 steps. Energy=    -452.4419066       time=      15.03
 Minus side of path:                    1473 steps. Energy=    -451.2817251       time=      16.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4419066  1.6434         -450.7985401 0.48319         -451.2817251  29.509  26.266   2.189  99.593
        Known (#5)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     14345.    
 decide> The unconnected minima in the chain and their distances are:
     4       24.30     6 
 

 tryconnect> 245-iteration DNEB run for minima 4_F and 6_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0555 Dev= 0.25% S= 25.32 time= 14.04
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=  43.42
 isnewts> transition state is the same as number        2 energy=     -450.7985401317
 tryconnect> Will not repeat search for TS      1 same as TS      2
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     21838.    
 decide> The unconnected minima in the chain and their distances are:
     5       27.95     6 
 

 tryconnect> 280-iteration DNEB run for minima 5_F and 6_S using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0637 Dev= 0.24% S= 29.20 time= 18.52
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  37.98

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1244 steps. Energy=    -452.4419066       time=      12.95
 Minus side of path:                    1277 steps. Energy=    -453.3006181       time=      13.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4419066 0.66209         -451.7798151  1.5208         -453.3006181   9.007   6.581  40.401   5.396
        Known (#5)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     19535.    
 decide> The unconnected minima in the chain and their distances are:
     7       26.93     6 
 

 tryconnect> 280-iteration DNEB run for minima 6_S and 7_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0168 Dev= 0.46% S= 27.33 time= 18.27
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  23.24

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1274 steps. Energy=    -451.3336395       time=      13.20
 Minus side of path:                    1279 steps. Energy=    -453.3006181       time=      13.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.3336395 0.37396E-01     -451.2962434  2.0044         -453.3006181  27.675  26.942   2.034 107.200
        Known (#6)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -450.1383146 0.77199        -449.3663245  1.9673        -451.3336395  64.458  32.919   2.176 100.201
   8     -451.3336395 0.37396E-01    -451.2962434  2.0044        -453.3006181  27.675  26.942   2.034 107.200
   7     -453.3006181  1.5208        -451.7798151 0.66209        -452.4419066   9.007   6.581  40.401   5.396
   2     -452.4419066  1.6434        -450.7985401 0.48319        -451.2817251  29.509  26.262   2.187  99.660
   3     -451.2817251  1.3089        -449.9728513 0.18259        -450.1554378  11.362  10.975   3.187  68.408

 Number of TS in the path       =      5
 Number of cycles               =      7

 Elapsed time=                               929.88
 OPTIM> # of energy calls=                        144 time=           1.07 %=  0.1
 OPTIM> # of energy+gradient calls=             70051 time=         538.23 %= 57.9
 OPTIM> # of energy+gradient+Hessian calls=       481 time=         142.93 %= 15.4
