
 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 17:41:52
  [-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:         0.05000       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=    -446.8212553     RMS force=    0.9625907686E-06
 OPTIM> Final energy  =    -447.3499946     RMS force=    0.9436101973E-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      148.9099424    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7294.9    
 decide> The unconnected minima in the chain and their distances are:
     2       19.25     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=   166
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> Backtracking      1 steps, current active atoms=   172
 intlbfgs> Backtracking      2 steps, current active atoms=   181
 intlbfgs> switch on true potential at step   1694 fraction=    0.990000 images=     3 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1719 steps, energy/image=    -79.19316864     RMS=30.50904037     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   30.52     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 315 RMS= 0.3292 Dev= 3.43% S= 30.36 time= 21.48
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  64.30

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1475 steps. Energy=    -447.0135420       time=      18.59
 Minus side of path:                    1315 steps. Energy=    -447.3016277       time=      16.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.0135420  2.8991         -444.1144223  3.1872         -447.3016277  29.075  22.909   8.239  26.460
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     10056.    
 decide> The unconnected minima in the chain and their distances are:
     2       19.80     3     4       13.09     1 
 

 tryconnect> Interpolation for minima 2_F and 3_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=   171
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     92 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    117 steps, energy/image=    -440.0115030     RMS=.2945703731     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   22.57     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0578 Dev= 0.76% S= 21.44 time= 9.61
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=  38.03

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1398 steps. Energy=    -447.3361682       time=      15.17
 Minus side of path:                    1342 steps. Energy=    -447.3499946       time=      15.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3361682  1.2839         -446.0522204  1.2978         -447.3499946  27.619  18.864  11.135  19.577
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_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=    -439.9832359     RMS=1.095132619     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   18.66     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 175 RMS= 0.0407 Dev= 1.07% S= 13.22 time= 6.56
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  30.30

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1298 steps. Energy=    -446.8212553       time=      15.80
 Minus side of path:                    1303 steps. Energy=    -447.3016277       time=      15.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8212553 0.13501         -446.6862468 0.61538         -447.3016277  14.381  13.089   8.591  25.374
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     10965.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.19     3 
 

 tryconnect> Interpolation for minima 3_S and 5_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=   121
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     98 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    123 steps, energy/image=    -431.5083865     RMS=4.582723644     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   26.41     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 245 RMS= 0.0445 Dev= 0.39% S= 22.48 time= 12.74
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         93
 DNEB run yielded 1 true transition state(s) time=  50.81

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1334 steps. Energy=    -447.0135420       time=      13.91
 Minus side of path:                    1388 steps. Energy=    -447.3361682       time=      14.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.0135420 0.62653E-01     -446.9508888 0.38528         -447.3361682  28.722  22.206   3.474  62.746
        Known (#3)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -446.8212553 0.13501        -446.6862468 0.61538        -447.3016277  14.381  13.089   8.591  25.374
   1     -447.3016277  3.1872        -444.1144223  2.8991        -447.0135420  29.075  22.909   8.239  26.460
   4     -447.0135420 0.62653E-01    -446.9508888 0.38528        -447.3361682  28.722  22.206   3.474  62.746
   2     -447.3361682  1.2839        -446.0522204  1.2978        -447.3499946  27.619  18.864  11.135  19.577

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                               364.73
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             23335 time=         172.46 %= 47.3
 OPTIM> # of energy+gradient+Hessian calls=       293 time=          82.46 %= 22.6
