
 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 22:12:15
  [-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=    -456.5122962     RMS force=    0.9666319537E-06
 OPTIM> Final energy  =    -455.7654914     RMS force=    0.9781028196E-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     1    2 from     0.38670E-03 to     0.45119E-03 ref=     1.0090    
 checkperc> Increasing con cutoff atoms     1    4 from     0.38731E-03 to     0.56303E-03 ref=     1.0092    
 checkperc> Increasing con cutoff atoms     1    5 from     0.22793E-02 to     0.23305E-02 ref=     1.4848    
 checkperc> Increasing con cutoff atoms     1    6 from     0.47102E-02 to     0.49509E-02 ref=     2.0984    
 checkperc> Increasing con cutoff atoms     2    6 from     0.12253E-02 to     0.18533E-02 ref=     2.9470    
 checkperc> Increasing con cutoff atoms     3    5 from     0.28901E-02 to     0.42975E-02 ref=     2.0699    
 checkperc> Increasing con cutoff atoms     5    6 from     0.56363E-03 to     0.65336E-03 ref=     1.0904    
 checkperc> Increasing con cutoff atoms     6   12 from     0.94948E-02 to     0.10674E-01 ref=     2.1259    
 checkperc> Increasing con cutoff atoms    12   16 from     0.24344E-01 to     0.24587E-01 ref=     2.5098    
 checkperc> Increasing con cutoff atoms    16   24 from     0.13308     to     0.15110     ref=     4.5632    
 checkperc> Increasing con cutoff atoms    19   22 from     0.11112     to     0.11118     ref=     2.7392    
 checkperc> Increasing con cutoff atoms    19   29 from     0.14237     to     0.15402     ref=     6.2254    
 checkperc> Increasing con cutoff atoms    19   30 from     0.14906     to     0.16064     ref=     7.3013    
 checkperc> Increasing con cutoff atoms    19   35 from     0.10669     to     0.11349     ref=     3.4094    
 checkperc> Increasing con cutoff atoms    20   22 from     0.86127E-01 to     0.14302     ref=     3.3048    
 checkperc> Increasing con cutoff atoms    20   23 from     0.13751     to     0.22580     ref=     3.7509    
 checkperc> Increasing con cutoff atoms    20   24 from     0.63058E-01 to     0.95134E-01 ref=     4.2841    
 checkperc> Increasing con cutoff atoms    20   25 from     0.84886E-01 to     0.14310     ref=     5.2385    
 checkperc> Increasing con cutoff atoms    20   27 from     0.60315E-01 to     0.65240E-01 ref=     5.2997    
 checkperc> Increasing con cutoff atoms    20   29 from     0.10492     to     0.16193     ref=     5.4692    
 checkperc> Increasing con cutoff atoms    20   30 from     0.11026     to     0.16859     ref=     6.5115    
 checkperc> Increasing con cutoff atoms    20   35 from     0.78073E-01 to     0.11854     ref=     2.8522    
 checkperc> Increasing con cutoff atoms    21   29 from     0.29683E-02 to     0.34285E-02 ref=     4.2912    
 checkperc> Increasing con cutoff atoms    21   30 from     0.29937E-02 to     0.34287E-02 ref=     5.3715    
 checkperc> Increasing con cutoff atoms    21   31 from     0.33255E-02 to     0.44274E-02 ref=     3.8855    
 checkperc> Increasing con cutoff atoms    21   32 from     0.43722E-02 to     0.60433E-02 ref=     4.7956    
 checkperc> Increasing con cutoff atoms    21   33 from     0.30076E-02 to     0.42820E-02 ref=     2.6548    
 checkperc> Increasing con cutoff atoms    21   34 from     0.44130E-02 to     0.70653E-02 ref=     2.9736    
 checkperc> Increasing con cutoff atoms    22   26 from     0.16039E-02 to     0.16577E-02 ref=     2.2826    
 checkperc> Increasing con cutoff atoms    22   27 from     0.20176E-02 to     0.31462E-02 ref=     3.6652    
 checkperc> Increasing con cutoff atoms    22   34 from     0.29040E-02 to     0.54448E-02 ref=     4.1911    
 checkperc> Increasing con cutoff atoms    23   26 from     0.23527E-02 to     0.25895E-02 ref=     3.3194    
 checkperc> Increasing con cutoff atoms    23   27 from     0.31198E-02 to     0.47599E-02 ref=     4.6675    
 checkperc> Increasing con cutoff atoms    23   28 from     0.75895E-02 to     0.97577E-02 ref=     5.0858    
 checkperc> Increasing con cutoff atoms    23   29 from     0.24557E-02 to     0.28476E-02 ref=     5.7150    
 checkperc> Increasing con cutoff atoms    23   30 from     0.31920E-02 to     0.34337E-02 ref=     6.7246    
 checkperc> Increasing con cutoff atoms    23   34 from     0.36344E-02 to     0.61012E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    24   26 from     0.10662E-02 to     0.22770E-02 ref=     1.3785    
 checkperc> Increasing con cutoff atoms    24   27 from     0.25343E-02 to     0.51348E-02 ref=     2.5532    
 checkperc> Increasing con cutoff atoms    24   29 from     0.20320E-02 to     0.42867E-02 ref=     3.7645    
 checkperc> Increasing con cutoff atoms    24   30 from     0.25681E-02 to     0.44076E-02 ref=     4.6887    
 checkperc> Increasing con cutoff atoms    24   31 from     0.29172E-02 to     0.32550E-02 ref=     4.1390    
 checkperc> Increasing con cutoff atoms    24   33 from     0.16194E-02 to     0.26077E-02 ref=     3.5423    
 checkperc> Increasing con cutoff atoms    25   26 from     0.67281E-02 to     0.86388E-02 ref=     2.1348    
 checkperc> Increasing con cutoff atoms    25   27 from     0.93044E-02 to     0.14910E-01 ref=     2.9313    
 checkperc> Increasing con cutoff atoms    25   28 from     0.12529E-01 to     0.19309E-01 ref=     2.8914    
 checkperc> Increasing con cutoff atoms    25   29 from     0.88902E-02 to     0.14943E-01 ref=     4.2910    
 checkperc> Increasing con cutoff atoms    25   30 from     0.95609E-02 to     0.16257E-01 ref=     5.0812    
 checkperc> Increasing con cutoff atoms    25   31 from     0.72587E-02 to     0.12938E-01 ref=     4.9072    
 checkperc> Increasing con cutoff atoms    25   32 from     0.86224E-02 to     0.11861E-01 ref=     5.9860    
 checkperc> Increasing con cutoff atoms    25   33 from     0.58754E-02 to     0.89780E-02 ref=     4.4778    
 checkperc> Increasing con cutoff atoms    26   33 from     0.12466E-02 to     0.16253E-02 ref=     2.4209    
 checkperc> Increasing con cutoff atoms    29   35 from     0.17678E-02 to     0.28960E-02 ref=     2.8542    
 checkperc> Increasing con cutoff atoms    30   35 from     0.21851E-02 to     0.33671E-02 ref=     3.9362    
 checkperc> Increasing con cutoff atoms    31   35 from     0.21128E-02 to     0.23068E-02 ref=     2.4568    
 checkperc> Increasing con cutoff atoms    32   35 from     0.30821E-02 to     0.33489E-02 ref=     3.4305    
 checkperc> Increasing con cutoff atoms    33   35 from     0.59619E-03 to     0.84029E-03 ref=     1.4130    
 checkperc> Increasing con cutoff atoms    76   79 from     0.12561E-01 to     0.14503E-01 ref=     2.0951    
 checkperc> Increasing con cutoff atoms    78   79 from     0.10006E-02 to     0.10068E-02 ref=     1.0907    
 checkperc> Increasing con cutoff atoms    83   85 from     0.14200E-02 to     0.14285E-02 ref=     1.0905    
 checkperc> Increasing con cutoff atoms    98  102 from     0.76482E-02 to     0.76642E-02 ref=     2.0336    
 checkperc> Increasing con cutoff atoms   176  188 from     0.43423E-01 to     0.43840E-01 ref=     6.6014    
 checkperc> Increasing con cutoff atoms   179  187 from     0.10908E-01 to     0.11490E-01 ref=     4.2988    
 checkperc> Increasing con cutoff atoms   179  188 from     0.10546E-01 to     0.14588E-01 ref=     5.3784    
 checkperc> Increasing con cutoff atoms   180  187 from     0.28501E-02 to     0.29479E-02 ref=     4.6472    
 checkperc> Increasing con cutoff atoms   180  188 from     0.35120E-02 to     0.62163E-02 ref=     5.6712    
 checkperc> Increasing con cutoff atoms   181  188 from     0.55296E-02 to     0.64487E-02 ref=     6.7220    
 checkperc> Increasing con cutoff atoms   184  185 from     0.68331E-03 to     0.88192E-03 ref=     1.4036    
 checkperc> Increasing con cutoff atoms   184  187 from     0.14406E-02 to     0.20676E-02 ref=     2.4219    
 checkperc> Increasing con cutoff atoms   184  188 from     0.25062E-02 to     0.50858E-02 ref=     3.4054    
 checkperc> Increasing con cutoff atoms   185  188 from     0.36352E-02 to     0.43024E-02 ref=     2.1611    
 checkperc> Increasing con cutoff atoms   187  188 from     0.87971E-03 to     0.23152E-02 ref=     1.0821    
 checkperc> Increasing con cutoff atoms   187  191 from     0.13202E-02 to     0.22954E-02 ref=     2.4443    
 checkperc> Increasing con cutoff atoms   187  193 from     0.78280E-02 to     0.80431E-02 ref=     2.8592    
 checkperc> Increasing con cutoff atoms   188  191 from     0.24248E-02 to     0.37549E-02 ref=     3.4227    
 checkperc> Increasing con cutoff atoms   188  193 from     0.77496E-02 to     0.10667E-01 ref=     3.9411    
 initialise> Interpolation metric value for minima 1 and 2 is      20.08554975    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     8126.8    
 decide> The unconnected minima in the chain and their distances are:
     2       20.09     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=   112
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    107 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    132 steps, energy/image=    -435.6860389     RMS=6.043291183     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   25.34     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.0526 Dev= 0.28% S= 20.49 time= 12.88
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=  27.60

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1237 steps. Energy=    -455.7654914       time=      15.21
 Minus side of path:                    1268 steps. Energy=    -456.5122962       time=      16.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.7654914 0.96705         -454.7984419  1.7139         -456.5122962  21.605  20.088   2.427  89.825
        Known (#2)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -456.5122962  1.7139        -454.7984419 0.96705        -455.7654914  21.605  20.088   2.427  89.825

 Number of TS in the path       =      1
 Number of cycles               =      1

 Elapsed time=                                72.99
 OPTIM> # of energy calls=                          2 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=              5552 time=          41.79 %= 57.3
 OPTIM> # of energy+gradient+Hessian calls=        25 time=           7.83 %= 10.7
