
 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 22:16:27
  [-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> 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=    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
 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=    -531.9818486     RMS force=    0.9938969474E-06
 OPTIM> Final energy  =    -533.2142990     RMS force=    0.9586451822E-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      56.75020077    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     15361.    
 decide> The unconnected minima in the chain and their distances are:
     2       24.80     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=    50
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    762 fraction=    0.990000 images=    11 time=       0.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    787 steps, energy/image=    -481.3532403     RMS=1.073534957     images=  11
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   79.73     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.1056 Dev= 7.09% S= 99.10 time= 37.81
 Following    5 images are candidates for TS:    4    8   12   17   22  
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         38
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         24
 DNEB run yielded 5 true transition state(s) time=  19.54

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     590 steps. Energy=    -531.9818486       time=       1.48
 Minus side of path:                     606 steps. Energy=    -533.1067087       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.9818486  4.9844         -526.9974381  6.1093         -533.1067087  23.623  21.152   5.557  19.254
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms    19   20 from     0.38602E-02 to     0.39334E-02 ref=     1.0123    
 checkperc> Increasing con cutoff atoms    26   29 from     0.93582E-02 to     0.10336E-01 ref=     2.1596    
 checkperc> Increasing con cutoff atoms    26   30 from     0.10999E-01 to     0.13954E-01 ref=     2.1542    
 checkperc> Increasing con cutoff atoms    57   74 from     0.33785E-01 to     0.34277E-01 ref=     3.8641    
 checkperc> Increasing con cutoff atoms    89   90 from     0.19364E-01 to     0.20255E-01 ref=     2.1330    
 checkperc> Increasing con cutoff atoms    89   92 from     0.13232     to     0.22329     ref=     2.4716    
 checkperc> Increasing con cutoff atoms    91   93 from     0.10189E-01 to     0.12430E-01 ref=     2.1427    
 checkperc> Increasing con cutoff atoms    91   98 from     0.14513E-01 to     0.20971E-01 ref=     4.8155    
 checkperc> Increasing con cutoff atoms    91   99 from     0.19347E-01 to     0.24500E-01 ref=     6.1502    
 checkperc> Increasing con cutoff atoms    92   93 from     0.16632E-01 to     0.18555E-01 ref=     2.1253    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     560 steps. Energy=    -533.1067087       time=       1.48
 Minus side of path:                     605 steps. Energy=    -534.5052847       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1067087 0.81094         -532.2957688  2.2095         -534.5052847  16.392  14.440   6.286  17.021
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     647 steps. Energy=    -534.5052847       time=       1.73
 Minus side of path:                     650 steps. Energy=    -534.6087975       time=       1.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5052847  5.7791         -528.7261568  5.8826         -534.6087975  20.887  10.411  15.176   7.050
        Known (#4)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    45   48 from     0.33066E-02 to     0.33186E-02 ref=     1.5326    
 checkperc> Increasing con cutoff atoms    49   50 from     0.57558E-02 to     0.57662E-02 ref=     2.1924    
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     911 steps. Energy=    -534.4559620       time=       2.82
 Minus side of path:                     629 steps. Energy=    -534.6950832       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4559620  2.3038         -532.1521521  2.5429         -534.6950832  27.032  19.299   3.758  28.472
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms    19   20 from     0.39334E-02 to     0.39928E-02 ref=     1.0123    
 checkperc> Increasing con cutoff atoms    88   92 from     0.90205E-02 to     0.12329E-01 ref=     2.1492    
 checkperc> Increasing con cutoff atoms    90   92 from     0.43009E-03 to     0.12427E-02 ref=     1.0909    
 checkperc> Increasing con cutoff atoms    91   92 from     0.80774E-02 to     0.82055E-02 ref=     1.7513    
 checkperc> Increasing con cutoff atoms    94   95 from     0.90299E-03 to     0.14599E-02 ref=     1.0825    
 checkperc> Increasing con cutoff atoms    95   96 from     0.29941E-02 to     0.36463E-02 ref=     2.1629    
 checkperc> Increasing con cutoff atoms    95   98 from     0.28810E-02 to     0.33435E-02 ref=     3.4244    
 checkperc> Increasing con cutoff atoms    42   48 from     0.29895E-01 to     0.29927E-01 ref=     2.5699    
 checkperc> Increasing con cutoff atoms    47   48 from     0.16365E-01 to     0.17242E-01 ref=     2.1462    
 checkperc> Increasing con cutoff atoms    49   50 from     0.57662E-02 to     0.58655E-02 ref=     2.1924    
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     664 steps. Energy=    -533.2142990       time=       1.77
 Minus side of path:                     893 steps. Energy=    -534.4559620       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2142990 0.59372         -532.6205790  1.8354         -534.4559620  26.883  24.481   3.949  27.094
        Known (#2)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     51.072    
 decide> The unconnected minima in the chain and their distances are:
     7        3.71     5 
 

 tryconnect> Interpolation for minima 5_S and 7_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=   104
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -529.1534925     RMS=.1763898949     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      5     7 dist=   4.158     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.0564 Dev= 0.34% S= 3.73 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.24

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     578 steps. Energy=    -534.6950832       time=       1.48
 Minus side of path:                     538 steps. Energy=    -534.6087975       time=       1.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6950832 0.21993         -534.4751510 0.13365         -534.6087975   3.893   3.707  11.229   9.529
        Known (#7)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -531.9818486  4.9844        -526.9974381  6.1093        -533.1067087  23.623  21.152   5.557  19.254
   2     -533.1067087 0.81094        -532.2957688  2.2095        -534.5052847  16.392  14.440   6.286  17.021
   3     -534.5052847  5.7791        -528.7261568  5.8826        -534.6087975  20.887  10.411  15.176   7.050
   6     -534.6087975 0.13365        -534.4751510 0.21993        -534.6950832   3.893   3.707  11.229   9.529
   4     -534.6950832  2.5429        -532.1521521  2.3038        -534.4559620  27.032  19.299   3.758  28.472
   5     -534.4559620  1.8354        -532.6205790 0.59372        -533.2142990  26.883  24.481   3.949  27.094

 Number of TS in the path       =      6
 Number of cycles               =      2

 Elapsed time=                                83.13
 OPTIM> # of energy calls=                          4 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             30515 time=          61.09 %= 73.5
 OPTIM> # of energy+gradient+Hessian calls=       166 time=           9.38 %= 11.3
