
 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 22:15:19
  [-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=    -453.9043630     RMS force=    0.8883349996E-06
 OPTIM> Final energy  =    -447.0232064     RMS force=    0.9146973276E-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    16   36 from     0.44278E-02 to     0.47125E-02 ref=     1.5454    
 checkperc> Increasing con cutoff atoms    18   23 from     0.97630E-02 to     0.10001E-01 ref=     2.8590    
 checkperc> Increasing con cutoff atoms    18   27 from     0.69953E-02 to     0.75011E-02 ref=     5.0991    
 checkperc> Increasing con cutoff atoms    18   29 from     0.10534E-01 to     0.10852E-01 ref=     5.4980    
 checkperc> Increasing con cutoff atoms    18   30 from     0.10630E-01 to     0.10858E-01 ref=     6.5749    
 checkperc> Increasing con cutoff atoms    18   31 from     0.12848E-01 to     0.14066E-01 ref=     4.7962    
 checkperc> Increasing con cutoff atoms    18   32 from     0.14109E-01 to     0.15996E-01 ref=     5.5209    
 checkperc> Increasing con cutoff atoms    18   33 from     0.13420E-01 to     0.14923E-01 ref=     3.4055    
 checkperc> Increasing con cutoff atoms    18   34 from     0.17450E-01 to     0.20675E-01 ref=     3.2265    
 checkperc> Increasing con cutoff atoms    18   35 from     0.78118E-02 to     0.83740E-02 ref=     2.6751    
 checkperc> Increasing con cutoff atoms    21   34 from     0.44130E-02 to     0.44413E-02 ref=     2.9736    
 checkperc> Increasing con cutoff atoms    23   34 from     0.36344E-02 to     0.40276E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    24   35 from     0.16543E-02 to     0.18980E-02 ref=     2.2183    
 checkperc> Increasing con cutoff atoms    26   29 from     0.12154E-02 to     0.15034E-02 ref=     2.4216    
 checkperc> Increasing con cutoff atoms    26   35 from     0.78530E-03 to     0.84876E-03 ref=     1.4283    
 checkperc> Increasing con cutoff atoms    28   30 from     0.38496E-02 to     0.40661E-02 ref=     2.4960    
 checkperc> Increasing con cutoff atoms    76   79 from     0.12561E-01 to     0.14832E-01 ref=     2.0951    
 checkperc> Increasing con cutoff atoms    76   89 from     0.36085E-01 to     0.37758E-01 ref=     2.4925    
 checkperc> Increasing con cutoff atoms    77   79 from     0.86912E-01 to     0.90674E-01 ref=     2.8993    
 checkperc> Increasing con cutoff atoms   104  106 from     0.89724E-02 to     0.11674E-01 ref=     3.1361    
 checkperc> Increasing con cutoff atoms   149  152 from     0.44230E-02 to     0.47418E-02 ref=     2.1595    
 checkperc> Increasing con cutoff atoms   152  153 from     0.50399E-02 to     0.58322E-02 ref=     2.1570    
 checkperc> Increasing con cutoff atoms   160  172 from     0.25930E-01 to     0.26164E-01 ref=     2.4555    
 checkperc> Increasing con cutoff atoms   176  182 from     0.89492E-02 to     0.89794E-02 ref=     3.6919    
 checkperc> Increasing con cutoff atoms   189  190 from     0.10859E-02 to     0.11177E-02 ref=     1.0814    
 initialise> Interpolation metric value for minima 1 and 2 is      41.05559629    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     68924.    
 decide> The unconnected minima in the chain and their distances are:
     2       40.96     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=    34
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    269 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    294 steps, energy/image=    -243.1226695     RMS=12.70525464     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   47.67     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.2017697586    
 Double-ended search iterations= 490 RMS= 0.0365 Dev= 1.46% S= 45.35 time= 51.40
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  32.14

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    2298 steps. Energy=    -453.3223001       time=      37.98
 Minus side of path:                    1325 steps. Energy=    -447.0232064       time=      14.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3223001  7.4106         -445.9117178  1.1115         -447.0232064  48.280  46.378   2.274  95.861
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    18   22 from     0.56307E-02 to     0.72970E-02 ref=     2.5338    
 checkperc> Increasing con cutoff atoms    18   23 from     0.10001E-01 to     0.13865E-01 ref=     2.8590    
 checkperc> Increasing con cutoff atoms    18   26 from     0.50240E-02 to     0.57827E-02 ref=     3.8121    
 checkperc> Increasing con cutoff atoms    18   27 from     0.75011E-02 to     0.10134E-01 ref=     5.0991    
 checkperc> Increasing con cutoff atoms    18   29 from     0.10852E-01 to     0.15497E-01 ref=     5.4980    
 checkperc> Increasing con cutoff atoms    18   30 from     0.10858E-01 to     0.15743E-01 ref=     6.5749    
 checkperc> Increasing con cutoff atoms    18   31 from     0.14066E-01 to     0.20060E-01 ref=     4.7962    
 checkperc> Increasing con cutoff atoms    18   32 from     0.15996E-01 to     0.22847E-01 ref=     5.5209    
 checkperc> Increasing con cutoff atoms    18   33 from     0.14923E-01 to     0.21134E-01 ref=     3.4055    
 checkperc> Increasing con cutoff atoms    18   34 from     0.20675E-01 to     0.28713E-01 ref=     3.2265    
 checkperc> Increasing con cutoff atoms    18   35 from     0.83740E-02 to     0.11058E-01 ref=     2.6751    
 checkperc> Increasing con cutoff atoms    21   33 from     0.30076E-02 to     0.34499E-02 ref=     2.6548    
 checkperc> Increasing con cutoff atoms    21   34 from     0.44413E-02 to     0.63347E-02 ref=     2.9736    
 checkperc> Increasing con cutoff atoms    22   34 from     0.29040E-02 to     0.38861E-02 ref=     4.1911    
 checkperc> Increasing con cutoff atoms    23   33 from     0.18876E-02 to     0.24577E-02 ref=     4.6796    
 checkperc> Increasing con cutoff atoms    23   34 from     0.40276E-02 to     0.62348E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    25   34 from     0.60206E-02 to     0.63338E-02 ref=     5.3614    
 checkperc> Increasing con cutoff atoms    26   29 from     0.15034E-02 to     0.16180E-02 ref=     2.4216    
 checkperc> Increasing con cutoff atoms    26   31 from     0.25343E-02 to     0.28385E-02 ref=     2.7870    
 checkperc> Increasing con cutoff atoms    26   32 from     0.39662E-02 to     0.41666E-02 ref=     3.8679    
 checkperc> Increasing con cutoff atoms    26   35 from     0.84876E-03 to     0.95041E-03 ref=     1.4283    
 checkperc> Increasing con cutoff atoms    27   28 from     0.12483E-02 to     0.16265E-02 ref=     1.0804    
 checkperc> Increasing con cutoff atoms    27   29 from     0.53012E-03 to     0.56260E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    27   33 from     0.19684E-02 to     0.22608E-02 ref=     2.8210    
 checkperc> Increasing con cutoff atoms    27   35 from     0.19455E-02 to     0.28620E-02 ref=     2.4820    
 checkperc> Increasing con cutoff atoms    28   29 from     0.27516E-02 to     0.40098E-02 ref=     2.1631    
 checkperc> Increasing con cutoff atoms    28   30 from     0.40661E-02 to     0.51418E-02 ref=     2.4960    
 checkperc> Increasing con cutoff atoms    28   31 from     0.25380E-02 to     0.38681E-02 ref=     3.4147    
 checkperc> Increasing con cutoff atoms    28   32 from     0.33087E-02 to     0.41822E-02 ref=     4.3086    
 checkperc> Increasing con cutoff atoms    28   33 from     0.29113E-02 to     0.36471E-02 ref=     3.9012    
 checkperc> Increasing con cutoff atoms    28   34 from     0.28671E-02 to     0.34084E-02 ref=     4.9817    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.14988E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    77   79 from     0.90674E-01 to     0.91054E-01 ref=     2.8993    
 checkperc> Increasing con cutoff atoms   104  106 from     0.11674E-01 to     0.11997E-01 ref=     3.1361    
 checkperc> Increasing con cutoff atoms   149  152 from     0.47418E-02 to     0.51449E-02 ref=     2.1595    
 checkperc> Increasing con cutoff atoms   152  153 from     0.58322E-02 to     0.59071E-02 ref=     2.1570    
 checkperc> Increasing con cutoff atoms   184  185 from     0.68331E-03 to     0.69589E-03 ref=     1.4036    
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1758.0    
 decide> The unconnected minima in the chain and their distances are:
     3       12.06     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=   181
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -448.5544045     RMS=.1021910716     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   12.63     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0469 Dev= 0.21% S= 12.08 time= 2.36
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  27.88

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1219 steps. Energy=    -453.3223001       time=      12.98
 Minus side of path:                    1223 steps. Energy=    -453.9043630       time=      13.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3223001 0.49317E-01     -453.2729834 0.63138         -453.9043630  12.635  12.058   3.453  63.135
        Known (#3)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -453.9043630 0.63138        -453.2729834 0.49317E-01    -453.3223001  12.635  12.058   3.453  63.135
   1     -453.3223001  7.4106        -445.9117178  1.1115        -447.0232064  48.280  46.378   2.274  95.861

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

 Elapsed time=                               195.49
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             16003 time=         118.56 %= 60.6
 OPTIM> # of energy+gradient+Hessian calls=        69 time=          20.98 %= 10.7
