
 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 05/23/2012 at 21:53:29
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -450.5085471     RMS force=    0.9930500033E-06
 OPTIM> Final energy  =    -446.1382124     RMS force=    0.9316177303E-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=    0.65365E+06
 decide> The unconnected minima in the chain and their distances are:
     2       86.79     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9705470377E-01
 Double-ended search iterations= 805 RMS= 0.0246 Dev= 5.98% S= 112.82 time= 142.20
 Following    2 images are candidates for TS:    4   17  
 Converged to TS (number of iterations):         63
 Converged to TS (number of iterations):         50
 DNEB run yielded 2 true transition state(s) time= 108.56

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1291 steps. Energy=    -453.3784643       time=      14.50
 Minus side of path:                    1303 steps. Energy=    -454.3043908       time=      14.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3784643  3.3491         -450.0293206  4.2751         -454.3043908  32.698  22.063   3.694  59.009
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1316 steps. Energy=    -447.3806191       time=      15.80
 Minus side of path:                    1298 steps. Energy=    -450.0661139       time=      15.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3806191  3.9699         -443.4107342  6.6554         -450.0661139  28.738  24.870  14.200  15.353
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.34793E+06
 decide> The unconnected minima in the chain and their distances are:
     2       69.67     5     6       21.34     1 
 

 tryconnect> 700-iteration DNEB run for minima 2_F and 5_U using 20 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1019074390    
 Double-ended search iterations= 700 RMS= 0.0244 Dev= 4.95% S= 78.10 time= 107.07
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  39.59

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    2085 steps. Energy=    -447.3806191       time=      27.59
 Minus side of path:                    1418 steps. Energy=    -446.1382124       time=      15.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3806191  2.7307         -444.6498767  1.4883         -446.1382124  81.661  69.994   1.434 151.970
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0689 Dev= 0.20% S= 22.28 time= 9.49
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=  59.65
 isnewts> transition state is the same as number        1 energy=     -450.0293205699
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1315 steps. Energy=    -453.3784643       time=      14.61
 Minus side of path:                    1288 steps. Energy=    -454.3043908       time=      14.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3784643  3.3491         -450.0293206  4.2751         -454.3043908  32.698  22.063   3.695  59.002
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     19437.    
 decide> The unconnected minima in the chain and their distances are:
     6       21.34     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 805 RMS= 0.0599 Dev= 4.80% S= 26.26 time= 139.28
 Following    2 images are candidates for TS:   10   22  
 Converged to TS (number of iterations):         55
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=  72.96
 isnewts> transition state is the same as number        1 energy=     -450.0293205699
 tryconnect> Will not repeat search for TS      1 same as TS      1

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1270 steps. Energy=    -450.0661139       time=      13.28
 Minus side of path:                    1286 steps. Energy=    -450.8645126       time=      13.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.0661139 0.17184         -449.8942698 0.97024         -450.8645126   1.418   1.309 174.918   1.246
        Known (#6)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     9427.0    
 decide> The unconnected minima in the chain and their distances are:
     7       21.12     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 7_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.6282 Dev= 0.09% S= 21.95 time= 9.46
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=  50.74
 isnewts> transition state is the same as number        1 energy=     -450.0293205699
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     18854.    
 decide> The unconnected minima in the chain and their distances are:
     7       21.12     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 7_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2729573622E-01
 Double-ended search iterations= 805 RMS= 0.0072 Dev= 4.24% S= 31.10 time= 138.59
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=  53.58
 isnewts> transition state is the same as number        1 energy=     -450.0293205694
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     37102.    
 decide> The unconnected minima in the chain and their distances are:
     5       33.35     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 5_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 350 RMS= 0.1072 Dev= 0.54% S= 40.39 time= 25.38
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=  40.94

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1560 steps. Energy=    -450.5085471       time=      17.56
 Minus side of path:                    1326 steps. Energy=    -448.1565702       time=      13.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.5085471  6.0729         -444.4356636  3.7209         -448.1565702  42.530  33.687  13.238  16.467
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2.1951    
 decide> The unconnected minima in the chain and their distances are:
     5        1.30     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0349 Dev= 0.43% S= 1.41 time= 1.06
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  19.02

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1286 steps. Energy=    -448.1565702       time=      13.36
 Minus side of path:                    1255 steps. Energy=    -447.3806191       time=      12.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.1565702 0.96170         -447.1948698 0.18575         -447.3806191   1.417   1.300 185.209   1.177
        Known (#8)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -450.5085471  6.0729        -444.4356636  3.7209        -448.1565702  42.530  33.687  13.238  16.467
   7     -448.1565702 0.96170        -447.1948698 0.18575        -447.3806191   1.417   1.300 185.209   1.177
   3     -447.3806191  2.7307        -444.6498767  1.4883        -446.1382124  81.661  69.994   1.434 151.970

 Number of TS in the path       =      3
 Number of cycles               =      7

 Elapsed time=                              1235.81
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            112380 time=         842.78 %= 68.2
 OPTIM> # of energy+gradient+Hessian calls=       537 time=         152.35 %= 12.3
