
 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 21:40:34
  [-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=    -449.2844312     RMS force=    0.9556936514E-06
 OPTIM> Final energy  =    -450.8822184     RMS force=    0.9527597147E-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=    0.48800E+06
 decide> The unconnected minima in the chain and their distances are:
     2       78.73     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.0366 Dev= 5.56% S= 94.64 time= 138.53
 Following    3 images are candidates for TS:    8   10   14  
 Converged to TS (number of iterations):         98
 Converged to TS (number of iterations):        102
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 2 true transition state(s) time= 269.32

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1356 steps. Energy=    -449.2844312       time=      14.65
 Minus side of path:                    1740 steps. Energy=    -450.6234375       time=      21.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2844312 0.14870         -449.1357352  1.4877         -450.6234375  66.431  64.504   1.645 132.525
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1477 steps. Energy=    -451.0234376       time=      17.02
 Minus side of path:                    1376 steps. Energy=    -449.7921846       time=      15.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0234376  1.8243         -449.1991171 0.59307         -449.7921846  46.896  45.643   1.780 122.462
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     70766.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.36     4     5        3.08     3 
 

 tryconnect> 420-iteration DNEB run for minima 2_F and 4_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0552 Dev= 0.99% S= 46.26 time= 37.87
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 125.70

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0909 Dev= 0.10% S= 3.16 time= 1.41
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  23.71

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1317 steps. Energy=    -449.7921846       time=      15.35
 Minus side of path:                    1315 steps. Energy=    -450.6234375       time=      15.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7921846 0.15294         -449.6392422 0.98420         -450.6234375   3.144   3.081   7.506  29.045
        Known (#5)                                              Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.11242E+06
 decide> The unconnected minima in the chain and their distances are:
     2       48.26     5 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 5_S using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1123529514    
 Double-ended search iterations= 490 RMS= 0.0477 Dev= 3.85% S= 56.26 time= 51.97
 Following    1 images are candidates for TS:    7  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 121.66
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.12142E+06
 decide> The unconnected minima in the chain and their distances are:
     2       49.52     3 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 3_S using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 490 RMS= 0.0595 Dev= 5.26% S= 57.51 time= 51.87
 Following    2 images are candidates for TS:    6    9  
 Converged to TS (number of iterations):        183
 Converged to TS (number of iterations):         64
 DNEB run yielded 2 true transition state(s) time= 144.70

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1337 steps. Energy=    -450.8822184       time=      14.01
 Minus side of path:                    1332 steps. Energy=    -450.3039609       time=      14.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8822184 0.65918         -450.2230363 0.80925E-01     -450.3039609  20.752  19.975   4.618  47.205
        Known (#2)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1492 steps. Energy=    -451.8494557       time=      17.11
 Minus side of path:                    1364 steps. Energy=    -450.6234375       time=      15.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.8494557  1.8207         -450.0288016 0.59464         -450.6234375  47.274  46.032   1.796 121.354
        *NEW* (Placed in 7)                                     Known (#3)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     82527.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.54     7 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 7_S using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0296 Dev= 3.22% S= 49.23 time= 44.51
 Following    1 images are candidates for TS:    6  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 117.46
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.12199E+06
 decide> The unconnected minima in the chain and their distances are:
     6       49.60     5 
 

 tryconnect> 490-iteration DNEB run for minima 5_S and 6_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0657 Dev= 3.24% S= 58.73 time= 51.18
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        103
 DNEB run yielded 1 true transition state(s) time=  58.85

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1394 steps. Energy=    -449.2851093       time=      14.96
 Minus side of path:                    1485 steps. Energy=    -450.4863083       time=      16.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2851093 0.59961         -448.6854987  1.8008         -450.4863083  46.575  45.095   1.872 116.467
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     63268.    
 decide> The unconnected minima in the chain and their distances are:
     2        2.34     9     9       39.84     4 
 

 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= 0.1336 Dev= 0.38% S= 2.47 time= 1.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  20.46

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1283 steps. Energy=    -450.8822184       time=      13.26
 Minus side of path:                    1293 steps. Energy=    -450.4863083       time=      13.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8822184 0.94628         -449.9359342 0.55037         -450.4863083   2.574   2.335  35.402   6.158
        Known (#2)                                              Known (#9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 4_S and 9_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0614 Dev= 0.71% S= 43.49 time= 31.93
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  27.56

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1373 steps. Energy=    -451.0234376       time=      14.83
 Minus side of path:                    1558 steps. Energy=    -450.4863083       time=      17.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0234376  2.4699         -448.5535578  1.9328         -450.4863083  44.731  39.937   3.263  66.816
        Known (#4)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -449.2844312 0.14870        -449.1357352  1.4877        -450.6234375  66.431  64.504   1.645 132.525
   3     -450.6234375 0.98420        -449.6392422 0.15294        -449.7921846   3.144   3.081   7.506  29.045
   2     -449.7921846 0.59307        -449.1991171  1.8243        -451.0234376  46.896  45.643   1.780 122.462
   8     -451.0234376  2.4699        -448.5535578  1.9328        -450.4863083  44.731  39.937   3.263  66.816
   7     -450.4863083 0.55037        -449.9359342 0.94628        -450.8822184   2.574   2.335  35.402   6.158

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

 Elapsed time=                              1570.58
 OPTIM> # of energy calls=                        210 time=           1.55 %=  0.1
 OPTIM> # of energy+gradient calls=             96002 time=         711.56 %= 45.3
 OPTIM> # of energy+gradient+Hessian calls=      1620 time=         459.97 %= 29.3
