
 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 17:43:04
  [-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=    -448.3476289     RMS force=    0.9976521663E-06
 OPTIM> Final energy  =    -448.1134084     RMS force=    0.9988218700E-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      41.52827479    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     57444.    
 decide> The unconnected minima in the chain and their distances are:
     2       38.54     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=    45
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    347 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    372 steps, energy/image=    -422.1275353     RMS=2.068652618     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   43.87     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 455 RMS= 0.0734 Dev= 10.90% S= 46.25 time= 44.08
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        137
 DNEB run yielded 1 true transition state(s) time=  73.34

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1946 steps. Energy=    -447.8340882       time=      27.47
 Minus side of path:                    1469 steps. Energy=    -448.1134084       time=      18.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8340882  1.8079         -446.0261638  2.0872         -448.1134084  66.281  54.315   2.916  74.758
        *NEW* (Placed in 3)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    14   17 from     0.20376E-01 to     0.20510E-01 ref=     2.0899    
 checkperc> Increasing con cutoff atoms    16   37 from     0.78578E-02 to     0.80573E-02 ref=     2.4213    
 checkperc> Increasing con cutoff atoms    40   44 from     0.24209E-01 to     0.24294E-01 ref=     2.5515    
 checkperc> Increasing con cutoff atoms    40   47 from     0.17796E-01 to     0.17834E-01 ref=     3.4882    
 checkperc> Increasing con cutoff atoms    81   85 from     0.51578E-01 to     0.52668E-01 ref=     2.4610    
 checkperc> Increasing con cutoff atoms   119  123 from     0.20908E-01 to     0.21209E-01 ref=     2.1503    
 checkperc> Increasing con cutoff atoms   176  177 from     0.14570E-02 to     0.14780E-02 ref=     1.0905    
 checkperc> Increasing con cutoff atoms   176  179 from     0.56350E-02 to     0.62952E-02 ref=     1.5027    
 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=     88259.    
 decide> The unconnected minima in the chain and their distances are:
     3       44.48     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=     7
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    286 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    311 steps, energy/image=    -336.2293389     RMS=8.011357094     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   47.80     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.2017697586    
 Double-ended search iterations= 490 RMS= 0.0415 Dev= 3.84% S= 48.80 time= 52.01
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=  61.04

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1297 steps. Energy=    -448.3476289       time=      16.42
 Minus side of path:                    1328 steps. Energy=    -448.5503865       time=      15.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3476289 0.13255         -448.2150796 0.33531         -448.5503865  44.023  42.816   1.695 128.642
        Known (#1)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   176  177 from     0.14780E-02 to     0.14801E-02 ref=     1.0905    
 checkperc> Increasing con cutoff atoms   176  179 from     0.62952E-02 to     0.63047E-02 ref=     1.5027    
 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      3 steps with      1 missing connections, weight=     481.99    
 decide> The unconnected minima in the chain and their distances are:
     3        7.83     4 
 

 tryconnect> Interpolation for minima 3_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=   206
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     40 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     65 steps, energy/image=    -438.0825257     RMS=3.006560546     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   17.68     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 0.1440 Dev= 0.82% S= 8.99 time= 6.56
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=  56.81

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1271 steps. Energy=    -448.5926556       time=      16.25
 Minus side of path:                    1274 steps. Energy=    -448.5271980       time=      16.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.5926556 0.99549E-01     -448.4931065 0.34091E-01     -448.5271980  12.913  12.730   2.279  95.649
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    93   96 from     0.12373E-01 to     0.12779E-01 ref=     2.1614    
 checkperc> Increasing con cutoff atoms   176  177 from     0.14806E-02 to     0.14835E-02 ref=     1.0905    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     963.98    
 decide> The unconnected minima in the chain and their distances are:
     3        7.83     4 
 

 tryconnect> Interpolation for minima 3_F and 4_S 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=   206
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     45 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     70 steps, energy/image=    -442.5824619     RMS=.2950737483     images=  15
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   13.66     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 805 RMS= 0.0516 Dev= 5.14% S= 14.00 time= 137.86
 Following    2 images are candidates for TS:   11   17  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):         17
 DNEB run yielded 2 true transition state(s) time=  45.14

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1265 steps. Energy=    -447.8340882       time=      13.31
 Minus side of path:                    1265 steps. Energy=    -448.5926556       time=      13.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8340882  3.2809         -444.5532369  4.0394         -448.5926556  11.553   9.404  20.131  10.829
        Known (#3)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1236 steps. Energy=    -448.5926556       time=      12.81
 Minus side of path:                    1269 steps. Energy=    -448.5503865       time=      13.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.5926556  4.9408         -443.6518957  4.8985         -448.5503865   7.661   6.496  44.513   4.897
        Known (#5)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -448.3476289 0.13255        -448.2150796 0.33531        -448.5503865  44.023  42.816   1.695 128.642
   5     -448.5503865  4.8985        -443.6518957  4.9408        -448.5926556   7.661   6.496  44.513   4.897
   4     -448.5926556  4.0394        -444.5532369  3.2809        -447.8340882  11.553   9.404  20.131  10.829
   1     -447.8340882  1.8079        -446.0261638  2.0872        -448.1134084  66.281  54.315   2.916  74.758

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

 Elapsed time=                               647.98
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             53220 time=         394.44 %= 60.9
 OPTIM> # of energy+gradient+Hessian calls=       371 time=         108.42 %= 16.7
