
 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 22:11:12
  [-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=    -455.3937659     RMS force=    0.9929377711E-06
 OPTIM> Final energy  =    -454.9524419     RMS force=    0.9510893074E-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

 checkperc> Increasing con cutoff atoms    20   36 from     0.91757E-01 to     0.92042E-01 ref=     2.7033    
 checkperc> Increasing con cutoff atoms    21   30 from     0.29937E-02 to     0.38618E-02 ref=     5.3715    
 checkperc> Increasing con cutoff atoms    29   30 from     0.77416E-03 to     0.11622E-02 ref=     1.0823    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.16677E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    29   35 from     0.17678E-02 to     0.24414E-02 ref=     2.8542    
 checkperc> Increasing con cutoff atoms    30   31 from     0.15610E-02 to     0.28347E-02 ref=     2.1624    
 checkperc> Increasing con cutoff atoms    30   33 from     0.16402E-02 to     0.32303E-02 ref=     3.4241    
 checkperc> Increasing con cutoff atoms    30   34 from     0.21544E-02 to     0.27694E-02 ref=     4.3093    
 checkperc> Increasing con cutoff atoms    30   35 from     0.21851E-02 to     0.34800E-02 ref=     3.9362    
 checkperc> Increasing con cutoff atoms    40   55 from     0.42108E-01 to     0.73957E-01 ref=     4.1623    
 checkperc> Increasing con cutoff atoms    50   55 from     0.84502E-01 to     0.12116     ref=     2.6938    
 checkperc> Increasing con cutoff atoms    53   55 from     0.94979E-01 to     0.96738E-01 ref=     2.9019    
 checkperc> Increasing con cutoff atoms    59   60 from     0.50640E-03 to     0.80677E-03 ref=     1.3524    
 checkperc> Increasing con cutoff atoms    59   61 from     0.18196E-02 to     0.22416E-02 ref=     2.1640    
 checkperc> Increasing con cutoff atoms    62   71 from     0.15035E-02 to     0.16370E-02 ref=     3.5435    
 checkperc> Increasing con cutoff atoms    62   72 from     0.61252E-02 to     0.61569E-02 ref=     4.3826    
 checkperc> Increasing con cutoff atoms    74   77 from     0.67716E-02 to     0.94018E-02 ref=     2.0201    
 checkperc> Increasing con cutoff atoms    78   84 from     0.13426     to     0.14352     ref=     2.8348    
 checkperc> Increasing con cutoff atoms   114  132 from     0.71174E-02 to     0.72410E-02 ref=     1.5468    
 checkperc> Increasing con cutoff atoms   116  132 from     0.41766E-01 to     0.43736E-01 ref=     2.5688    
 checkperc> Increasing con cutoff atoms   122  130 from     0.80215E-01 to     0.86427E-01 ref=     2.7730    
 checkperc> Increasing con cutoff atoms   126  129 from     0.63996E-01 to     0.67975E-01 ref=     2.4249    
 checkperc> Increasing con cutoff atoms   148  149 from     0.46376E-02 to     0.46696E-02 ref=     2.1641    
 initialise> Interpolation metric value for minima 1 and 2 is      39.00353057    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     50202.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.85     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=    44
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    408 fraction=    0.990000 images=     5 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    433 steps, energy/image=    -426.1473822     RMS=.9029181100     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   46.74     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0488 Dev= 2.95% S= 43.84 time= 51.44
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        135
 DNEB run yielded 1 true transition state(s) time=  70.90

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1185 steps. Energy=    -455.9771915       time=      13.17
 Minus side of path:                    1182 steps. Energy=    -455.3937659       time=      13.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.9771915 0.99578         -454.9814084 0.41236         -455.3937659  35.659  35.179   2.496  87.354
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    22   30 from     0.25477E-02 to     0.28433E-02 ref=     5.6726    
 checkperc> Increasing con cutoff atoms    26   30 from     0.18611E-02 to     0.22769E-02 ref=     3.4056    
 checkperc> Increasing con cutoff atoms    27   29 from     0.53012E-03 to     0.64688E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    27   30 from     0.15137E-02 to     0.19168E-02 ref=     2.1611    
 checkperc> Increasing con cutoff atoms    41   42 from     0.11067E-01 to     0.11266E-01 ref=     2.1405    
 checkperc> Increasing con cutoff atoms    54   55 from     0.16561E-02 to     0.24624E-02 ref=     1.0902    
 checkperc> Increasing con cutoff atoms    59   72 from     0.22220E-01 to     0.22222E-01 ref=     2.9915    
 checkperc> Increasing con cutoff atoms    65   70 from     0.30352E-02 to     0.30821E-02 ref=     3.4094    
 checkperc> Increasing con cutoff atoms    71   73 from     0.17041E-02 to     0.17301E-02 ref=     1.4149    
 checkperc> Increasing con cutoff atoms   141  150 from     0.13591E-01 to     0.13786E-01 ref=     5.3802    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     37891.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.55     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=   115
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    109 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    134 steps, energy/image=    -446.2106475     RMS=.5801197841     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   36.29     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0428 Dev= 0.85% S= 36.23 time= 26.02
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=  45.35

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1310 steps. Energy=    -454.9524419       time=      15.36
 Minus side of path:                    1201 steps. Energy=    -454.5987264       time=      14.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.9524419 0.39041         -454.5620278 0.36699E-01     -454.5987264  18.141  16.717   5.982  36.445
        Known (#2)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    16   26 from     0.11048     to     0.12797     ref=     4.6747    
 checkperc> Increasing con cutoff atoms    16   28 from     0.13416     to     0.16242     ref=     6.7568    
 checkperc> Increasing con cutoff atoms    19   26 from     0.56814E-01 to     0.76531E-01 ref=     4.3852    
 checkperc> Increasing con cutoff atoms    19   27 from     0.88137E-01 to     0.11485     ref=     5.7173    
 checkperc> Increasing con cutoff atoms    19   28 from     0.62740E-01 to     0.92908E-01 ref=     6.5162    
 checkperc> Increasing con cutoff atoms    19   29 from     0.14237     to     0.16864     ref=     6.2254    
 checkperc> Increasing con cutoff atoms    19   30 from     0.14906     to     0.17899     ref=     7.3013    
 checkperc> Increasing con cutoff atoms    19   35 from     0.10669     to     0.11613     ref=     3.4094    
 checkperc> Increasing con cutoff atoms    22   27 from     0.20176E-02 to     0.20666E-02 ref=     3.6652    
 checkperc> Increasing con cutoff atoms    22   33 from     0.14967E-02 to     0.15043E-02 ref=     3.6457    
 checkperc> Increasing con cutoff atoms    22   34 from     0.29040E-02 to     0.39575E-02 ref=     4.1911    
 checkperc> Increasing con cutoff atoms    23   33 from     0.18876E-02 to     0.24325E-02 ref=     4.6796    
 checkperc> Increasing con cutoff atoms    23   34 from     0.36344E-02 to     0.50983E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    23   35 from     0.16646E-02 to     0.16788E-02 ref=     3.3007    
 checkperc> Increasing con cutoff atoms    24   34 from     0.27112E-02 to     0.29537E-02 ref=     4.3768    
 checkperc> Increasing con cutoff atoms    29   31 from     0.53786E-03 to     0.57591E-03 ref=     1.4063    
 checkperc> Increasing con cutoff atoms    39   41 from     0.10299     to     0.10434     ref=     2.8916    
 checkperc> Increasing con cutoff atoms    40   52 from     0.19969E-01 to     0.20062E-01 ref=     2.4482    
 checkperc> Increasing con cutoff atoms   114  132 from     0.72410E-02 to     0.72585E-02 ref=     1.5468    
 checkperc> Increasing con cutoff atoms   116  118 from     0.15955E-02 to     0.16473E-02 ref=     1.0907    
 checkperc> Increasing con cutoff atoms   132  134 from     0.32997E-02 to     0.33768E-02 ref=     1.3383    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     9942.2    
 decide> The unconnected minima in the chain and their distances are:
     4       21.48     3 
 

 tryconnect> Interpolation for minima 3_S and 4_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=   153
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     66 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     91 steps, energy/image=    -437.1948169     RMS=7.588465598     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   26.25     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 245 RMS= 0.0474 Dev= 0.60% S= 21.87 time= 12.81
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  27.70

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1176 steps. Energy=    -454.5987264       time=      13.85
 Minus side of path:                    1207 steps. Energy=    -455.9771915       time=      14.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.5987264 0.94484E-02     -454.5892779  1.3879         -455.9771915  21.683  21.482   5.430  40.145
        Known (#4)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -455.3937659 0.41236        -454.9814084 0.99578        -455.9771915  35.659  35.179   2.496  87.354
   3     -455.9771915  1.3879        -454.5892779 0.94484E-02    -454.5987264  21.683  21.482   5.430  40.145
   2     -454.5987264 0.36699E-01    -454.5620278 0.39041        -454.9524419  18.141  16.717   5.982  36.445

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

 Elapsed time=                               323.40
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             23386 time=         173.15 %= 53.5
 OPTIM> # of energy+gradient+Hessian calls=       248 time=          70.74 %= 21.9
