
 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=    -447.8514456     RMS force=    0.9627212904E-06
 OPTIM> Final energy  =    -447.8184902     RMS force=    0.9638383070E-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      26.00048193    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     9495.9    
 decide> The unconnected minima in the chain and their distances are:
     2       21.15     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=   108
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    192 fraction=    0.990000 images=     3 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    217 steps, energy/image=    -434.7845885     RMS=1.030711286     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   26.70     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1347 Dev= 4.68% S= 28.12 time= 16.89
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        208
 DNEB run yielded 1 true transition state(s) time= 124.25

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    2558 steps. Energy=    -455.4679472       time=      41.48
 Minus side of path:                    1507 steps. Energy=    -446.9436562       time=      17.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.4679472  8.8785         -446.5894654 0.35419         -446.9436562  74.136  66.705   1.929 113.013
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms     1    5 from     0.19273E-02 to     0.20337E-02 ref=     1.4845    
 checkperc> Increasing con cutoff atoms     1    6 from     0.21063E-02 to     0.30136E-02 ref=     2.1000    
 checkperc> Increasing con cutoff atoms     2    4 from     0.15702E-02 to     0.24919E-02 ref=     1.6386    
 checkperc> Increasing con cutoff atoms     2   13 from     0.14408     to     0.15280     ref=     3.8898    
 checkperc> Increasing con cutoff atoms     2   16 from     0.14430     to     0.15832     ref=     5.6941    
 checkperc> Increasing con cutoff atoms     3    4 from     0.65953E-02 to     0.92575E-02 ref=     1.6453    
 checkperc> Increasing con cutoff atoms     3    5 from     0.58072E-02 to     0.13801E-01 ref=     2.0734    
 checkperc> Increasing con cutoff atoms     3    6 from     0.19165E-01 to     0.35103E-01 ref=     2.3681    
 checkperc> Increasing con cutoff atoms     3    7 from     0.35951E-02 to     0.70727E-02 ref=     3.3710    
 checkperc> Increasing con cutoff atoms     3    9 from     0.43964E-02 to     0.12232E-01 ref=     4.1967    
 checkperc> Increasing con cutoff atoms     4    5 from     0.18501E-02 to     0.20635E-02 ref=     2.0693    
 checkperc> Increasing con cutoff atoms     4    6 from     0.11216E-02 to     0.12553E-02 ref=     2.9464    
 checkperc> Increasing con cutoff atoms     4    7 from     0.25815E-01 to     0.29483E-01 ref=     2.7611    
 checkperc> Increasing con cutoff atoms     4   10 from     0.33835E-01 to     0.55006E-01 ref=     3.2477    
 checkperc> Increasing con cutoff atoms     4   11 from     0.38716E-01 to     0.59968E-01 ref=     4.0213    
 checkperc> Increasing con cutoff atoms     5    8 from     0.13766E-02 to     0.20032E-02 ref=     2.1690    
 checkperc> Increasing con cutoff atoms     6   10 from     0.12973E-01 to     0.14648E-01 ref=     2.6473    
 checkperc> Increasing con cutoff atoms     6   11 from     0.12970E-01 to     0.13816E-01 ref=     3.5278    
 checkperc> Increasing con cutoff atoms     7   12 from     0.99169E-02 to     0.13873E-01 ref=     2.5166    
 checkperc> Increasing con cutoff atoms     8   12 from     0.20160E-01 to     0.29517E-01 ref=     2.7599    
 checkperc> Increasing con cutoff atoms    10   12 from     0.59476E-02 to     0.84357E-02 ref=     3.7630    
 checkperc> Increasing con cutoff atoms    10   13 from     0.14706     to     0.14941     ref=     4.3757    
 checkperc> Increasing con cutoff atoms    11   12 from     0.87792E-02 to     0.12102E-01 ref=     4.4725    
 checkperc> Increasing con cutoff atoms    13   15 from     0.22203E-02 to     0.30923E-02 ref=     3.1438    
 checkperc> Increasing con cutoff atoms    16   41 from     0.50835E-01 to     0.58304E-01 ref=     4.1962    
 checkperc> Increasing con cutoff atoms    17   18 from     0.17152E-01 to     0.21388E-01 ref=     2.1370    
 checkperc> Increasing con cutoff atoms    80   84 from     0.70814E-02 to     0.83322E-02 ref=     2.1548    
 checkperc> Increasing con cutoff atoms    80   86 from     0.17278E-01 to     0.18387E-01 ref=     2.5326    
 checkperc> Increasing con cutoff atoms    91   94 from     0.13181E-01 to     0.13289E-01 ref=     2.0845    
 checkperc> Increasing con cutoff atoms    93   95 from     0.37592E-02 to     0.38353E-02 ref=     1.5417    
 checkperc> Increasing con cutoff atoms    94   95 from     0.13727E-01 to     0.16774E-01 ref=     2.1424    
 checkperc> Increasing con cutoff atoms    94   97 from     0.10715E-01 to     0.11103E-01 ref=     3.0439    
 checkperc> Increasing con cutoff atoms   100  102 from     0.38019E-02 to     0.38104E-02 ref=     1.0119    
 checkperc> Increasing con cutoff atoms   134  138 from     0.29900E-01 to     0.32996E-01 ref=     2.4547    
 checkperc> Increasing con cutoff atoms   173  174 from     0.12271E-01 to     0.12751E-01 ref=     2.1264    
 checkperc> Increasing con cutoff atoms   196  200 from     0.27848E-01 to     0.29825E-01 ref=     2.4876    
 checkperc> Increasing con cutoff atoms   198  200 from     0.32843E-02 to     0.34773E-02 ref=     1.5443    
 checkperc> Increasing con cutoff atoms   200  206 from     0.57390E-01 to     0.57596E-01 ref=     2.5803    
 checkperc> Increasing con cutoff atoms   173  174 from     0.12751E-01 to     0.15008E-01 ref=     2.1264    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     18992.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.15     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   108
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    187 fraction=    0.990000 images=    15 time=       1.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    212 steps, energy/image=    -439.7709000     RMS=.9967458599     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   33.48     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 805 RMS= 0.3430 Dev= 6.49% S= 31.69 time= 138.76
 Following    1 images are candidates for TS:   15  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=  50.21

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1410 steps. Energy=    -447.8514456       time=      16.57
 Minus side of path:                    1781 steps. Energy=    -446.9436562       time=      23.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8514456  3.8191         -444.0323617  2.9113         -446.9436562  52.820  47.129   3.149  69.220
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     41895.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.69     4 
 

 tryconnect> Interpolation for minima 2_F and 4_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=    43
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    326 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    351 steps, energy/image=    -437.1825694     RMS=2.690094162     images=   5
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   39.29     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0306 Dev= 1.09% S= 38.09 time= 31.58
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  36.82

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1393 steps. Energy=    -447.8184902       time=      15.31
 Minus side of path:                    1745 steps. Energy=    -446.9436562       time=      21.16

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8184902  2.2068         -445.6117051  1.3320         -446.9436562  51.912  34.880   3.155  69.102
        Known (#2)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -447.8514456  3.8191        -444.0323617  2.9113        -446.9436562  52.820  47.129   3.149  69.220
   3     -446.9436562  1.3320        -445.6117051  2.2068        -447.8184902  51.912  34.880   3.155  69.102

 Number of TS in the path       =      2
 Number of cycles               =      3

 Elapsed time=                               541.95
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             41003 time=         303.76 %= 56.1
 OPTIM> # of energy+gradient+Hessian calls=       340 time=         100.63 %= 18.6
