
 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 22:13:48
  [-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=    -450.4012162     RMS force=    0.9749658453E-06
 OPTIM> Final energy  =    -452.6647550     RMS force=    0.9765606674E-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      145.9230672    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.36127E+06
 decide> The unconnected minima in the chain and their distances are:
     2       71.08     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=     4
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1688 fraction=    0.990000 images=    11 time=       3.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1713 steps, energy/image=    -407.4268693     RMS=2.207089815     images=  12
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   86.98     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.1433940004    
 Double-ended search iterations= 805 RMS= 0.1726 Dev= 4.01% S= 93.73 time= 137.66
 Following    2 images are candidates for TS:   11   22  
 Converged to TS (number of iterations):        147
 Converged to TS (number of iterations):         27
 DNEB run yielded 2 true transition state(s) time=  99.96

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1475 steps. Energy=    -450.3431493       time=      16.16
 Minus side of path:                    1710 steps. Energy=    -450.4217329       time=      20.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3431493  1.9082         -448.4349393  1.9868         -450.4217329  72.767  61.936   3.026  72.046
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    36   39 from     0.10112E-01 to     0.10470E-01 ref=     2.0195    
 checkperc> Increasing con cutoff atoms    37   39 from     0.74926E-02 to     0.76955E-02 ref=     3.1429    
 checkperc> Increasing con cutoff atoms    61   62 from     0.28406E-02 to     0.30221E-02 ref=     2.1920    
 checkperc> Increasing con cutoff atoms    61   65 from     0.53697E-02 to     0.53835E-02 ref=     4.6640    
 checkperc> Increasing con cutoff atoms    62   69 from     0.29507E-02 to     0.29679E-02 ref=     4.1392    
 checkperc> Increasing con cutoff atoms    62   70 from     0.29806E-02 to     0.29942E-02 ref=     5.2188    
 checkperc> Increasing con cutoff atoms    62   71 from     0.18087E-02 to     0.18657E-02 ref=     3.5427    
 checkperc> Increasing con cutoff atoms    93  106 from     0.42286E-01 to     0.43559E-01 ref=     2.5707    
 checkperc> Increasing con cutoff atoms   114  135 from     0.42792E-01 to     0.43006E-01 ref=     2.5465    
 checkperc> Increasing con cutoff atoms   147  151 from     0.37877E-02 to     0.43010E-02 ref=     2.4298    
 checkperc> Increasing con cutoff atoms   147  153 from     0.40879E-02 to     0.42266E-02 ref=     2.8190    
 checkperc> Increasing con cutoff atoms   147  154 from     0.69242E-02 to     0.71728E-02 ref=     3.8970    
 checkperc> Increasing con cutoff atoms   148  153 from     0.67330E-02 to     0.68063E-02 ref=     3.8973    
 checkperc> Increasing con cutoff atoms   148  154 from     0.77247E-02 to     0.78963E-02 ref=     4.9772    
 checkperc> Increasing con cutoff atoms    52   53 from     0.21069E-02 to     0.21288E-02 ref=     1.0087    
 checkperc> Increasing con cutoff atoms   114  134 from     0.21164E-01 to     0.21232E-01 ref=     2.4615    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1177 steps. Energy=    -453.3642410       time=      11.66
 Minus side of path:                    1177 steps. Energy=    -452.6647550       time=      11.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3642410  2.9864         -450.3778242  2.2869         -452.6647550   7.065   6.389  33.517   6.504
        *NEW* (Placed in 5)                                     Known (#2)
 checkperc> Increasing con cutoff atoms     1    6 from     0.21063E-02 to     0.21517E-02 ref=     2.1000    
 checkperc> Increasing con cutoff atoms     4    6 from     0.11216E-02 to     0.11900E-02 ref=     2.9464    
 checkperc> Increasing con cutoff atoms     5   14 from     0.39717E-02 to     0.40972E-02 ref=     2.4508    
 checkperc> Increasing con cutoff atoms     6   36 from     0.13191     to     0.13706     ref=     4.7877    
 checkperc> Increasing con cutoff atoms    12   14 from     0.29907E-02 to     0.30393E-02 ref=     1.3413    
 checkperc> Increasing con cutoff atoms    13   15 from     0.22203E-02 to     0.22871E-02 ref=     3.1438    
 checkperc> Increasing con cutoff atoms    14   15 from     0.34986E-02 to     0.35426E-02 ref=     1.0148    
 checkperc> Increasing con cutoff atoms    14   37 from     0.11729     to     0.11917     ref=     2.8572    
 checkperc> Increasing con cutoff atoms    37   38 from     0.57828E-02 to     0.87161E-02 ref=     2.2639    
 checkperc> Increasing con cutoff atoms    44   46 from     0.12530E-02 to     0.12787E-02 ref=     1.0891    
 checkperc> Increasing con cutoff atoms    54   74 from     0.45587E-02 to     0.48241E-02 ref=     1.5434    
 checkperc> Increasing con cutoff atoms    80   86 from     0.17278E-01 to     0.17671E-01 ref=     2.5326    
 checkperc> Increasing con cutoff atoms    83   86 from     0.35383E-02 to     0.36223E-02 ref=     1.5348    
 checkperc> Increasing con cutoff atoms    83   87 from     0.11271E-01 to     0.11512E-01 ref=     2.4098    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     13339.    
 decide> The unconnected minima in the chain and their distances are:
     5       22.03     3     4       13.76     1 
 

 tryconnect> Interpolation for minima 3_U and 5_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=   161
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     59 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     84 steps, energy/image=    -443.8739169     RMS=1.853006516     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   27.79     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.7174272199    
 Double-ended search iterations= 280 RMS= 0.1456 Dev= 2.85% S= 23.15 time= 16.60
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  30.46

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1274 steps. Energy=    -453.3642410       time=      13.31
 Minus side of path:                    1249 steps. Energy=    -450.3431493       time=      12.89

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.3642410  3.1625         -450.2017830 0.14137         -450.3431493  23.302  22.040   6.990  31.187
        Known (#5)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_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=   141
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     78 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    103 steps, energy/image=    -444.8109136     RMS=.6252589365     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   19.92     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 0.0461 Dev= 0.22% S= 13.79 time= 6.52
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  38.19

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1277 steps. Energy=    -450.4012162       time=      13.40
 Minus side of path:                    1251 steps. Energy=    -450.4033488       time=      12.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4012162 0.36499E-01     -450.3647170 0.38632E-01     -450.4033488   9.591   9.312   2.975  73.269
        Known (#1)                                              *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms    93   94 from     0.21302E-02 to     0.21374E-02 ref=     1.0896    
 checkperc> Increasing con cutoff atoms   105  110 from     0.46300E-01 to     0.47677E-01 ref=     2.5022    
 checkperc> Increasing con cutoff atoms   148  151 from     0.68428E-02 to     0.68552E-02 ref=     3.4124    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     182.81    
 decide> The unconnected minima in the chain and their distances are:
     4        5.67     6 
 

 tryconnect> Interpolation for minima 4_F and 6_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=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -445.8751022     RMS=.1794056195     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      4     6 dist=   6.008     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0240 Dev= 0.05% S= 5.67 time= 1.05
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  18.53

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1218 steps. Energy=    -450.4217329       time=      12.44
 Minus side of path:                    1246 steps. Energy=    -450.4033488       time=      12.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4217329 0.24142E-01     -450.3975905 0.57583E-02     -450.4033488   5.732   5.670   2.259  96.490
        Known (#4)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -450.4012162 0.36499E-01    -450.3647170 0.38632E-01    -450.4033488   9.591   9.312   2.975  73.269
   5     -450.4033488 0.57583E-02    -450.3975905 0.24142E-01    -450.4217329   5.732   5.670   2.259  96.490
   1     -450.4217329  1.9868        -448.4349393  1.9082        -450.3431493  72.767  61.936   3.026  72.046
   3     -450.3431493 0.14137        -450.2017830  3.1625        -453.3642410  23.302  22.040   6.990  31.187
   2     -453.3642410  2.9864        -450.3778242  2.2869        -452.6647550   7.065   6.389  33.517   6.504

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                               494.90
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             41674 time=         306.99 %= 62.0
 OPTIM> # of energy+gradient+Hessian calls=       297 time=          83.75 %= 16.9
