
 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 17:42:57
  [-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=    -446.1530152     RMS force=    0.9137454401E-06
 OPTIM> Final energy  =    -449.9035338     RMS force=    0.9103043442E-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      58.25778996    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.18829E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.26     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=     5
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    585 fraction=    0.990000 images=     7 time=       1.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    610 steps, energy/image=    -420.1067376     RMS=.6507848845     images=   8
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   63.63     Attempts, images and iterations=     0    19   665
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 665 RMS= 0.0667 Dev= 3.74% S= 66.88 time= 95.05
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        240
 DNEB run yielded 1 true transition state(s) time= 137.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1360 steps. Energy=    -447.7706511       time=      17.03
 Minus side of path:                    1674 steps. Energy=    -449.0573647       time=      24.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7706511 0.22305         -447.5476012  1.5098         -449.0573647  55.212  44.638   1.886 115.619
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms     1   10 from     0.87773E-02 to     0.87892E-02 ref=     2.8596    
 checkperc> Increasing con cutoff atoms     1   11 from     0.93085E-02 to     0.93480E-02 ref=     3.7709    
 checkperc> Increasing con cutoff atoms     2    3 from     0.22601E-02 to     0.22616E-02 ref=     1.6386    
 checkperc> Increasing con cutoff atoms     2    7 from     0.25852E-01 to     0.25857E-01 ref=     2.6502    
 checkperc> Increasing con cutoff atoms     2    8 from     0.39312E-01 to     0.39321E-01 ref=     3.0361    
 checkperc> Increasing con cutoff atoms     2    9 from     0.19195E-01 to     0.19197E-01 ref=     3.6367    
 checkperc> Increasing con cutoff atoms     2   10 from     0.28201E-01 to     0.28205E-01 ref=     2.4680    
 checkperc> Increasing con cutoff atoms     2   11 from     0.32149E-01 to     0.32266E-01 ref=     3.3727    
 checkperc> Increasing con cutoff atoms     3   11 from     0.18639E-01 to     0.18715E-01 ref=     4.6949    
 checkperc> Increasing con cutoff atoms     3   12 from     0.17834E-01 to     0.17864E-01 ref=     2.7297    
 checkperc> Increasing con cutoff atoms    76   80 from     0.19028E-01 to     0.19085E-01 ref=     2.4798    
 checkperc> Increasing con cutoff atoms    82   83 from     0.14175E-01 to     0.14287E-01 ref=     2.1403    
 checkperc> Increasing con cutoff atoms    83   85 from     0.17907E-02 to     0.17993E-02 ref=     1.0902    
 checkperc> Increasing con cutoff atoms     1    4 from     0.37858E-03 to     0.37967E-03 ref=     1.0089    
 checkperc> Increasing con cutoff atoms     2    6 from     0.19102E-01 to     0.19118E-01 ref=     2.3976    
 checkperc> Increasing con cutoff atoms     2    7 from     0.25857E-01 to     0.25865E-01 ref=     2.6502    
 checkperc> Increasing con cutoff atoms     2    8 from     0.39321E-01 to     0.39397E-01 ref=     3.0361    
 checkperc> Increasing con cutoff atoms     3   10 from     0.20256E-01 to     0.20266E-01 ref=     3.7464    
 checkperc> Increasing con cutoff atoms   117  119 from     0.19404E-01 to     0.19514E-01 ref=     2.1510    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.15170E+06
 decide> The unconnected minima in the chain and their distances are:
     2       33.09     3     3       48.63     1 
 

 tryconnect> Interpolation for minima 2_F and 3_U 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=    27
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    208 fraction=    0.990000 images=     3 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    233 steps, energy/image=    -437.6619425     RMS=.5484148525     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   37.25     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0433 Dev= 1.59% S= 35.43 time= 32.42
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        134
 DNEB run yielded 1 true transition state(s) time=  80.08
 isnewts> transition state is the same as number        1 energy=     -447.5476012410
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1360 steps. Energy=    -447.7706511       time=      14.52
 Minus side of path:                    1676 steps. Energy=    -449.0573647       time=      19.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7706511 0.22305         -447.5476012  1.5098         -449.0573647  55.210  44.644   1.883 115.768
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 3_U 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=    11
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    280 fraction=    0.990000 images=     5 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    305 steps, energy/image=    -436.2602585     RMS=.8147880613     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   50.48     Attempts, images and iterations=     0    15   525
 lbfgs> Final DNEB force constant     0.1433940004    
 Double-ended search iterations= 525 RMS= 0.0338 Dev= 5.41% S= 52.52 time= 58.96
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):         26
 DNEB run yielded 2 true transition state(s) time=  49.79

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1288 steps. Energy=    -449.1300467       time=      13.46
 Minus side of path:                    1269 steps. Energy=    -446.1530152       time=      13.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.1300467  3.3600         -445.7700564 0.38296         -446.1530152   5.484   5.052  42.260   5.159
        *NEW* (Placed in 5)                                     Known (#1)
 checkperc> Increasing con cutoff atoms   107  113 from     0.55784E-01 to     0.55788E-01 ref=     2.5585    
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1624 steps. Energy=    -447.7706511       time=      19.09
 Minus side of path:                    1343 steps. Energy=    -449.1300467       time=      14.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7706511 0.42009         -447.3505607  1.7795         -449.1300467  49.797  48.253   1.667 130.765
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     72650.    
 decide> The unconnected minima in the chain and their distances are:
     2       33.09     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=    27
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    203 fraction=    0.990000 images=    15 time=       2.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    228 steps, energy/image=    -365.0107206     RMS=14.80680994     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   45.17     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.6569044378E-01
 Double-ended search iterations= 805 RMS= 0.0209 Dev= 3.54% S= 39.41 time= 138.77
 Following    1 images are candidates for TS:   16  
 Converged to TS (number of iterations):        124
 DNEB run yielded 1 true transition state(s) time=  64.42
 isnewts> transition state is the same as number        1 energy=     -447.5476012251
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.14823E+06
 decide> The unconnected minima in the chain and their distances are:
     2       52.87     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=    18
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    587 fraction=    0.990000 images=     6 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    612 steps, energy/image=    -170.7352822     RMS=13.57003805     images=   7
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   56.87     Attempts, images and iterations=     0    17   595
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.0128 Dev= 1.00% S= 55.74 time= 75.91
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=  20.24

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1467 steps. Energy=    -449.9035338       time=      16.23
 Minus side of path:                    1364 steps. Energy=    -449.0573647       time=      14.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9035338  1.4407         -448.4628354 0.59453         -449.0573647  54.301  52.931   2.057 105.955
        Known (#2)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -446.1530152 0.38296        -445.7700564  3.3600        -449.1300467   5.484   5.052  42.260   5.159
   4     -449.1300467  1.7795        -447.3505607 0.42009        -447.7706511  49.797  48.253   1.667 130.765
   1     -447.7706511 0.22305        -447.5476012  1.5098        -449.0573647  55.212  44.638   1.886 115.619
   5     -449.0573647 0.59453        -448.4628354  1.4407        -449.9035338  54.301  52.931   2.057 105.955

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

 Elapsed time=                               935.75
 OPTIM> # of energy calls=                         10 time=           0.08 %=  0.0
 OPTIM> # of energy+gradient calls=             77591 time=         577.22 %= 61.7
 OPTIM> # of energy+gradient+Hessian calls=       570 time=         169.38 %= 18.1
