
 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 22:13:58
  [-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=    -447.6268301     RMS force=    0.9384062946E-06
 OPTIM> Final energy  =    -449.3686196     RMS force=    0.9156143465E-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      48.48692603    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.11306E+06
 decide> The unconnected minima in the chain and their distances are:
     2       48.31     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=    12
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    391 fraction=    0.990000 images=     4 time=       1.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    416 steps, energy/image=    -370.1627991     RMS=13.06803694     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   49.68     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0407 Dev= 3.78% S= 53.45 time= 51.81
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  64.98

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1289 steps. Energy=    -449.3686196       time=      16.05
 Minus side of path:                    1304 steps. Energy=    -450.2634452       time=      15.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3686196 0.54259E-01     -449.3143610 0.94908         -450.2634452  13.531  12.606   4.136  52.706
        Known (#2)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   162  168 from     0.29287E-02 to     0.29970E-02 ref=     1.4153    
 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=    0.11413E+06
 decide> The unconnected minima in the chain and their distances are:
     3       48.46     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=     9
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    479 fraction=    0.990000 images=     6 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    504 steps, energy/image=    -345.6082591     RMS=6.312110326     images=   7
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   61.76     Attempts, images and iterations=     0    18   630
 lbfgs> Final DNEB force constant     0.2981058282    
 Double-ended search iterations= 630 RMS= 0.0238 Dev= 3.38% S= 53.79 time= 85.89
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        110
 DNEB run yielded 1 true transition state(s) time=  62.07

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1337 steps. Energy=    -447.7721702       time=      14.00
 Minus side of path:                    1332 steps. Energy=    -447.6268301       time=      14.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7721702 0.44076         -447.3314121 0.29542         -447.6268301  40.809  38.436   1.707 127.740
        *NEW* (Placed in 4)                                     Known (#1)
 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=     6749.2    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     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=   100
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    144 fraction=    0.990000 images=     3 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    169 steps, energy/image=    -375.3055761     RMS=13.42297921     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   24.18     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1894 Dev= 2.96% S= 22.03 time= 12.91
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 134.73
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     9398.7    
 decide> The unconnected minima in the chain and their distances are:
     3       21.08     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=    75
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    252 fraction=    0.990000 images=     3 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    277 steps, energy/image=     257.8502530     RMS=27.04419490     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   27.28     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0563 Dev= 3.25% S= 27.03 time= 16.64
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=  37.09

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1295 steps. Energy=    -447.7721702       time=      13.23
 Minus side of path:                    1308 steps. Energy=    -448.6323677       time=      13.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7721702 0.78073E-01     -447.6940976 0.93827         -448.6323677  13.839  12.347   4.092  53.271
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     6784.3    
 decide> The unconnected minima in the chain and their distances are:
     3       18.91     5 
 

 tryconnect> Interpolation for minima 3_F and 5_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=   104
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    320 fraction=    0.990000 images=     3 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    345 steps, energy/image=    -314.9544941     RMS=14.96990420     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   23.72     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0891 Dev= 3.13% S= 22.31 time= 12.79
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        166
 DNEB run yielded 1 true transition state(s) time=  80.89

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1421 steps. Energy=    -448.6323677       time=      15.29
 Minus side of path:                    1489 steps. Energy=    -449.6344052       time=      16.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6323677 0.55187         -448.0804974  1.5539         -449.6344052  53.354  51.567   2.081 104.761
        Known (#5)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     13498.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     4 
 

 tryconnect> Interpolation for minima 2_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=   100
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    195 fraction=    0.990000 images=    15 time=       1.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    220 steps, energy/image=    -385.5407386     RMS=10.46506758     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   29.20     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 805 RMS= 0.0316 Dev= 5.39% S= 28.80 time= 136.87
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=  32.13

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1600 steps. Energy=    -450.2634452       time=      18.02
 Minus side of path:                    1363 steps. Energy=    -447.6268301       time=      14.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2634452  7.9892         -442.2742282  5.3526         -447.6268301  50.726  48.465   1.782 122.356
        Known (#3)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -447.6268301  5.3526        -442.2742282  7.9892        -450.2634452  50.726  48.465   1.782 122.356
   1     -450.2634452 0.94908        -449.3143610 0.54259E-01    -449.3686196  13.531  12.606   4.136  52.706

 Number of TS in the path       =      2
 Number of cycles               =      6

 Elapsed time=                               892.50
 OPTIM> # of energy calls=                         12 time=           0.09 %=  0.0
 OPTIM> # of energy+gradient calls=             66628 time=         491.44 %= 55.1
 OPTIM> # of energy+gradient+Hessian calls=       730 time=         203.48 %= 22.8
