
 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 05/27/2012 at 22:09:45
  [-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> Constraint potential parameters read from file congeom.dat
 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -450.5726244     RMS force=    0.9655337902E-06
 OPTIM> Final energy  =    -451.7697439     RMS force=    0.9969703124E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      90.04507585    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.27130E+06
 decide> The unconnected minima in the chain and their distances are:
     2       64.65     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=     4
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1223 fraction=    0.990000 images=     7 time=       2.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1248 steps, energy/image=    -372.2502972     RMS=1.639234253     images=   8
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   77.68     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 805 RMS= 0.0674 Dev= 5.12% S= 78.57 time= 138.88
 Following    2 images are candidates for TS:    8   15  
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         50
 DNEB run yielded 2 true transition state(s) time=  65.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1430 steps. Energy=    -450.5726244       time=      18.11
 Minus side of path:                    1566 steps. Energy=    -451.6665611       time=      22.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.5726244 0.54267         -450.0299583  1.6366         -451.6665611  55.443  53.352   2.209  98.686
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    93   95 from     0.37592E-02 to     0.38772E-02 ref=     1.5417    
 checkperc> Increasing con cutoff atoms    93   97 from     0.81941E-02 to     0.95067E-02 ref=     2.1619    
 checkperc> Increasing con cutoff atoms    94   97 from     0.10715E-01 to     0.10920E-01 ref=     3.0439    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1445 steps. Energy=    -451.6152627       time=      21.83
 Minus side of path:                    1460 steps. Energy=    -451.1230994       time=      20.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6152627  6.1700         -445.4452738  5.6778         -451.1230994  41.479  27.692   6.184  35.254
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms   161  170 from     0.19726E-01 to     0.22953E-01 ref=     2.1223    
 checkperc> Increasing con cutoff atoms   172  174 from     0.54629E-02 to     0.64462E-02 ref=     1.4700    
 checkperc> Increasing con cutoff atoms   173  174 from     0.12271E-01 to     0.13649E-01 ref=     2.1264    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     11985.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.85     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    95
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    256 fraction=    0.990000 images=     5 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    281 steps, energy/image=    -426.2840730     RMS=1.425708332     images=   5
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   37.43     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 385 RMS= 0.1041 Dev= 4.76% S= 32.36 time= 31.83
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  47.36

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1520 steps. Energy=    -452.4517835       time=      17.92
 Minus side of path:                    1426 steps. Energy=    -451.6152627       time=      17.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4517835  6.9074         -445.5443654  6.0709         -451.6152627  38.588  24.582   6.106  35.705
        *NEW* (Placed in 6)                                     Known (#4)
 checkperc> Increasing con cutoff atoms   196  197 from     0.14680E-02 to     0.14975E-02 ref=     1.0110    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     12162.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.88     4     4       11.79     3 
 

 tryconnect> Interpolation for minima 2_F and 4_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   125
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    211 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    236 steps, energy/image=    -304.8631006     RMS=13.86683718     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   33.40     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 350 RMS= 0.0900 Dev= 2.91% S= 27.34 time= 26.35
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  43.94
 isnewts> transition state is the same as number        3 energy=     -445.5443653583
 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:                    1529 steps. Energy=    -452.4517835       time=      18.37
 Minus side of path:                    1422 steps. Energy=    -451.6152627       time=      16.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4517835  6.9074         -445.5443654  6.0709         -451.6152627  38.588  24.584   6.087  35.811
        Known (#6)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 3_S and 4_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   187
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     32 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     57 steps, energy/image=    -446.8632145     RMS=.7680838268E-01 images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   12.93     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0213 Dev= 0.15% S= 11.80 time= 2.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  31.48

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1322 steps. Energy=    -451.6665611       time=      15.06
 Minus side of path:                    1321 steps. Energy=    -451.6152627       time=      14.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6665611 0.61518E-01     -451.6050429 0.10220E-01     -451.6152627  11.956  11.788   2.613  83.423
        Known (#3)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     21039.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.88     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   125
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    218 fraction=    0.990000 images=    15 time=       1.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    243 steps, energy/image=    -444.5427337     RMS=1.346378201     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   34.29     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.5098621309    
 Double-ended search iterations= 805 RMS= 0.0267 Dev= 5.46% S= 39.24 time= 138.69
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=  31.21
 isnewts> transition state is the same as number        3 energy=     -445.5443653583
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     23970.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.85     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    95
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    235 fraction=    0.990000 images=    16 time=       1.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    260 steps, energy/image=    -439.4067003     RMS=1.685552230     images=  16
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   40.87     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      5.846792891    
 Double-ended search iterations= 805 RMS= 0.6621 Dev= 5.08% S= 30.42 time= 138.36
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=  40.63

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1471 steps. Energy=    -451.7697439       time=      16.01
 Minus side of path:                    1374 steps. Energy=    -451.6665611       time=      14.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7697439  6.4001         -445.3696697  6.2969         -451.6665611  33.991  22.875   3.182  68.515
        Known (#2)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -450.5726244 0.54267        -450.0299583  1.6366        -451.6665611  55.443  53.352   2.209  98.686
   6     -451.6665611  6.2969        -445.3696697  6.4001        -451.7697439  33.991  22.875   3.182  68.515

 Number of TS in the path       =      2
 Number of cycles               =      5

 Elapsed time=                               965.49
 OPTIM> # of energy calls=                         12 time=           0.09 %=  0.0
 OPTIM> # of energy+gradient calls=             92889 time=         689.68 %= 71.4
 OPTIM> # of energy+gradient+Hessian calls=       328 time=          92.15 %=  9.5
