
 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 17:43:18
  [-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=    -443.6015210     RMS force=    0.9895854949E-06
 OPTIM> Final energy  =    -441.7497927     RMS force=    0.9126847264E-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      40.48843796    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     63571.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.87     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=    88
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    177 fraction=    0.990000 images=     4 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    202 steps, energy/image=    -428.5219538     RMS=.4861932244     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   42.27     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0628 Dev= 4.55% S= 46.76 time= 37.76
 Following    2 images are candidates for TS:    3   10  
 Converged to TS (number of iterations):         35
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 142.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1321 steps. Energy=    -443.6015210       time=      14.04
 Minus side of path:                    1559 steps. Energy=    -444.5880173       time=      17.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.6015210 0.36888         -443.2326441  1.3554         -444.5880173  40.499  34.226   4.315  50.517
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   136  160 from     0.33340E-01 to     0.35569E-01 ref=     3.8890    
 checkperc> Increasing con cutoff atoms   158  161 from     0.19663E-01 to     0.23620E-01 ref=     2.0941    
 checkperc> Increasing con cutoff atoms   158  162 from     0.38152E-01 to     0.40981E-01 ref=     2.4985    
 checkperc> Increasing con cutoff atoms   161  162 from     0.22796E-01 to     0.24354E-01 ref=     2.1299    
 checkperc> Increasing con cutoff atoms   172  175 from     0.20181E-01 to     0.20398E-01 ref=     2.0859    
 checkperc> Increasing con cutoff atoms   172  194 from     0.39684E-01 to     0.42146E-01 ref=     2.5052    
 checkperc> Increasing con cutoff atoms   187  191 from     0.16419E-02 to     0.19718E-02 ref=     2.4447    
 checkperc> Increasing con cutoff atoms   188  191 from     0.36703E-02 to     0.47039E-02 ref=     3.4237    
 checkperc> Increasing con cutoff atoms   189  191 from     0.90848E-03 to     0.10468E-02 ref=     1.4088    
 checkperc> Increasing con cutoff atoms   195  197 from     0.68825E-02 to     0.78421E-02 ref=     3.1378    
 checkperc> Increasing con cutoff atoms   196  197 from     0.14038E-02 to     0.16312E-02 ref=     1.0115    
 checkperc> Increasing con cutoff atoms   200  202 from     0.12723E-02 to     0.13417E-02 ref=     1.0903    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     4222.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.15     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=   168
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     63 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     88 steps, energy/image=    -432.0684544     RMS=.7347428258     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   17.17     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 175 RMS= 0.0931 Dev= 1.29% S= 17.64 time= 6.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        113
 DNEB run yielded 1 true transition state(s) time=  59.05

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1271 steps. Energy=    -444.6863347       time=      13.13
 Minus side of path:                    1288 steps. Energy=    -444.6669414       time=      13.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.6863347 0.57979         -444.1065449 0.56040         -444.6669414  14.152  13.787  11.952  18.239
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms   157  158 from     0.13075E-01 to     0.13687E-01 ref=     2.2607    
 checkperc> Increasing con cutoff atoms   158  170 from     0.63585E-01 to     0.72129E-01 ref=     2.5080    
 checkperc> Increasing con cutoff atoms   160  174 from     0.36703E-01 to     0.38860E-01 ref=     3.8527    
 checkperc> Increasing con cutoff atoms   161  162 from     0.24354E-01 to     0.25355E-01 ref=     2.1299    
 checkperc> Increasing con cutoff atoms   161  170 from     0.32320E-01 to     0.32326E-01 ref=     2.1101    
 checkperc> Increasing con cutoff atoms   162  168 from     0.42700E-02 to     0.43079E-02 ref=     1.4153    
 checkperc> Increasing con cutoff atoms   172  174 from     0.51594E-02 to     0.57518E-02 ref=     1.4691    
 checkperc> Increasing con cutoff atoms   174  194 from     0.67019E-02 to     0.68458E-02 ref=     1.5458    
 checkperc> Increasing con cutoff atoms   174  198 from     0.21372E-01 to     0.27320E-01 ref=     3.8780    
 checkperc> Increasing con cutoff atoms   176  194 from     0.37314E-01 to     0.38509E-01 ref=     2.5580    
 checkperc> Increasing con cutoff atoms   180  188 from     0.44508E-02 to     0.48568E-02 ref=     5.6714    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4654.5    
 decide> The unconnected minima in the chain and their distances are:
     2       14.22     4     4       12.08     3 
 

 tryconnect> Interpolation for minima 2_F and 4_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=   181
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     78 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    103 steps, energy/image=    -378.8335782     RMS=17.22611415     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   20.82     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 210 RMS= 0.1665 Dev= 0.94% S= 16.05 time= 9.39
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  29.98

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1267 steps. Energy=    -441.7497927       time=      13.07
 Minus side of path:                    1285 steps. Energy=    -444.6863347       time=      13.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -441.7497927  2.3512         -439.3986164  5.2877         -444.6863347  21.462  14.302   6.814  31.991
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 3_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=   181
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     38 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     63 steps, energy/image=    -431.8227949     RMS=4.300137279     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   17.51     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 175 RMS= 0.0769 Dev= 0.68% S= 12.27 time= 6.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  29.02

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1307 steps. Energy=    -444.6863347       time=      13.56
 Minus side of path:                    1348 steps. Energy=    -444.5880173       time=      14.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.6863347 0.74725         -443.9390823 0.64894         -444.5880173  25.060  12.232   4.784  45.564
        Known (#4)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -443.6015210 0.36888        -443.2326441  1.3554        -444.5880173  40.499  34.226   4.315  50.517
   4     -444.5880173 0.64894        -443.9390823 0.74725        -444.6863347  25.060  12.232   4.784  45.564
   3     -444.6863347  5.2877        -439.3986164  2.3512        -441.7497927  21.462  14.302   6.814  31.991

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

 Elapsed time=                               437.48
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             25890 time=         192.07 %= 43.9
 OPTIM> # of energy+gradient+Hessian calls=       478 time=         128.48 %= 29.4
