
 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 17:42:44
  [-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=    -443.1945211     RMS force=    0.9219927188E-06
 OPTIM> Final energy  =    -449.7446477     RMS force=    0.8911615976E-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      55.42123987    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.15051E+06
 decide> The unconnected minima in the chain and their distances are:
     2       53.14     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=     2
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    594 fraction=    0.990000 images=     6 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    619 steps, energy/image=    -431.1123842     RMS=.6915595380     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   60.86     Attempts, images and iterations=     0    18   630
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 630 RMS= 0.0704 Dev= 4.43% S= 61.64 time= 84.65
 Following    2 images are candidates for TS:    9   15  
 Converged to TS (number of iterations):         34
 Converged to TS (number of iterations):        198
 DNEB run yielded 2 true transition state(s) time= 205.46

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1274 steps. Energy=    -449.7872410       time=      13.58
 Minus side of path:                    1252 steps. Energy=    -448.6083710       time=      13.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7872410  3.3529         -446.4343612  2.1740         -448.6083710   9.763   7.599  19.962  10.921
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    37   39 from     0.59469E-02 to     0.59506E-02 ref=     3.1447    
 checkperc> Increasing con cutoff atoms    54   55 from     0.20401E-02 to     0.20445E-02 ref=     1.0894    
 checkperc> Increasing con cutoff atoms    61   62 from     0.30064E-02 to     0.30120E-02 ref=     2.1925    
 checkperc> Increasing con cutoff atoms    61   65 from     0.55492E-02 to     0.55695E-02 ref=     4.6649    
 checkperc> Increasing con cutoff atoms    61   66 from     0.99234E-02 to     0.99558E-02 ref=     5.0798    
 checkperc> Increasing con cutoff atoms    61   68 from     0.34380E-02 to     0.34602E-02 ref=     6.7235    
 checkperc> Increasing con cutoff atoms    62   64 from     0.13506E-02 to     0.13538E-02 ref=     1.3784    
 checkperc> Increasing con cutoff atoms    62   68 from     0.44058E-02 to     0.44366E-02 ref=     4.6872    
 checkperc> Increasing con cutoff atoms    62   69 from     0.30376E-02 to     0.30501E-02 ref=     4.1397    
 checkperc> Increasing con cutoff atoms    62   70 from     0.29584E-02 to     0.29755E-02 ref=     5.2192    
 checkperc> Increasing con cutoff atoms    63   69 from     0.50033E-02 to     0.50205E-02 ref=     4.9023    
 checkperc> Increasing con cutoff atoms    63   70 from     0.50918E-02 to     0.51150E-02 ref=     5.9825    
 checkperc> Increasing con cutoff atoms    64   65 from     0.39347E-03 to     0.39894E-03 ref=     1.4036    
 checkperc> Increasing con cutoff atoms    64   66 from     0.78924E-03 to     0.79270E-03 ref=     2.1603    
 checkperc> Increasing con cutoff atoms    64   68 from     0.71567E-03 to     0.73241E-03 ref=     3.4067    
 checkperc> Increasing con cutoff atoms    64   69 from     0.28680E-02 to     0.28817E-02 ref=     2.7873    
 checkperc> Increasing con cutoff atoms    64   70 from     0.28558E-02 to     0.28747E-02 ref=     3.8695    
 checkperc> Increasing con cutoff atoms    65   67 from     0.91628E-03 to     0.92224E-03 ref=     1.4047    
 checkperc> Increasing con cutoff atoms    65   69 from     0.24485E-02 to     0.24522E-02 ref=     2.4311    
 checkperc> Increasing con cutoff atoms    66   69 from     0.21468E-02 to     0.21479E-02 ref=     3.4151    
 checkperc> Increasing con cutoff atoms    68   69 from     0.27051E-03 to     0.28081E-03 ref=     2.1624    
 checkperc> Increasing con cutoff atoms   142  151 from     0.50498E-02 to     0.51606E-02 ref=     4.6352    
 checkperc> Increasing con cutoff atoms   143  149 from     0.69889E-02 to     0.72374E-02 ref=     5.7104    
 checkperc> Increasing con cutoff atoms   143  150 from     0.75589E-02 to     0.78510E-02 ref=     6.7196    
 checkperc> Increasing con cutoff atoms   176  178 from     0.17166E-02 to     0.18339E-02 ref=     1.0903    
 checkperc> Increasing con cutoff atoms   216  217 from     0.84076E-03 to     0.86677E-03 ref=     1.2537    
 checkperc> Increasing con cutoff atoms    45   46 from     0.18713E-02 to     0.19022E-02 ref=     1.7775    
 checkperc> Increasing con cutoff atoms    65   67 from     0.92224E-03 to     0.92535E-03 ref=     1.4047    
 checkperc> Increasing con cutoff atoms    65   70 from     0.23091E-02 to     0.24022E-02 ref=     3.4104    
 checkperc> Increasing con cutoff atoms    66   69 from     0.21479E-02 to     0.21497E-02 ref=     3.4151    
 checkperc> Increasing con cutoff atoms    84   87 from     0.75036E-01 to     0.83691E-01 ref=     3.2202    
 checkperc> Increasing con cutoff atoms    84   88 from     0.81040E-01 to     0.87201E-01 ref=     2.5867    
 checkperc> Increasing con cutoff atoms    85   87 from     0.13720     to     0.13870     ref=     2.6587    
 checkperc> Increasing con cutoff atoms    85   88 from     0.12568     to     0.12701     ref=     3.1591    
 checkperc> Increasing con cutoff atoms   138  150 from     0.64187E-01 to     0.64253E-01 ref=     6.6104    
 checkperc> Increasing con cutoff atoms   142  149 from     0.41551E-02 to     0.43191E-02 ref=     4.6461    
 checkperc> Increasing con cutoff atoms   143  149 from     0.72374E-02 to     0.73701E-02 ref=     5.7104    
 checkperc> Increasing con cutoff atoms   143  150 from     0.78510E-02 to     0.81960E-02 ref=     6.7196    
 checkperc> Increasing con cutoff atoms   146  149 from     0.20550E-02 to     0.20763E-02 ref=     2.4214    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1276 steps. Energy=    -449.7872410       time=      13.20
 Minus side of path:                    1249 steps. Energy=    -448.8418385       time=      12.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7872410  1.0128         -448.7744796 0.67359E-01     -448.8418385  25.707  22.256   3.106  70.196
        Known (#3)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    37   39 from     0.59506E-02 to     0.61088E-02 ref=     3.1447    
 checkperc> Increasing con cutoff atoms    64   66 from     0.79270E-03 to     0.79405E-03 ref=     2.1603    
 checkperc> Increasing con cutoff atoms    68   69 from     0.28081E-03 to     0.36991E-03 ref=     2.1624    
 checkperc> Increasing con cutoff atoms   141  143 from     0.62735E-02 to     0.80430E-02 ref=     2.1666    
 checkperc> Increasing con cutoff atoms   142  145 from     0.92607E-02 to     0.12705E-01 ref=     2.1166    
 checkperc> Increasing con cutoff atoms   142  149 from     0.43191E-02 to     0.62534E-02 ref=     4.6461    
 checkperc> Increasing con cutoff atoms   142  151 from     0.51606E-02 to     0.54793E-02 ref=     4.6352    
 checkperc> Increasing con cutoff atoms   143  144 from     0.72928E-02 to     0.13182E-01 ref=     2.1882    
 checkperc> Increasing con cutoff atoms   143  145 from     0.16452E-01 to     0.31636E-01 ref=     2.5597    
 checkperc> Increasing con cutoff atoms   143  146 from     0.67426E-02 to     0.87706E-02 ref=     3.3149    
 checkperc> Increasing con cutoff atoms   143  147 from     0.10723E-01 to     0.11800E-01 ref=     4.6601    
 checkperc> Increasing con cutoff atoms   143  149 from     0.73701E-02 to     0.11111E-01 ref=     5.7104    
 checkperc> Increasing con cutoff atoms   143  150 from     0.81960E-02 to     0.13772E-01 ref=     6.7196    
 checkperc> Increasing con cutoff atoms   144  153 from     0.29222E-02 to     0.53417E-02 ref=     3.5413    
 checkperc> Increasing con cutoff atoms   144  155 from     0.48372E-02 to     0.62171E-02 ref=     2.2192    
 checkperc> Increasing con cutoff atoms   146  149 from     0.20763E-02 to     0.33922E-02 ref=     2.4214    
 checkperc> Increasing con cutoff atoms   166  167 from     0.41196E-02 to     0.41652E-02 ref=     1.7755    
 checkperc> Increasing con cutoff atoms   176  178 from     0.18339E-02 to     0.21107E-02 ref=     1.0903    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.13664E+06
 decide> The unconnected minima in the chain and their distances are:
     2       13.78     3     4       51.12     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=   203
 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=    -430.0376149     RMS=5.809471987     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   21.03     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 210 RMS= 0.1121 Dev= 1.15% S= 15.56 time= 9.35
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  22.70

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1261 steps. Energy=    -449.7446477       time=      12.92
 Minus side of path:                    1267 steps. Energy=    -449.7872410       time=      13.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7446477  4.7831         -444.9615041  4.8257         -449.7872410  15.678  13.792  15.617  13.959
        Known (#2)                                              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=     2
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    543 fraction=    0.990000 images=     5 time=       1.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    568 steps, energy/image=    -436.2405994     RMS=.6626822305     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   51.64     Attempts, images and iterations=     0    15   525
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0241 Dev= 2.19% S= 53.54 time= 58.24
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  30.32

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1392 steps. Energy=    -443.1945211       time=      15.19
 Minus side of path:                    1428 steps. Energy=    -448.6083710       time=      15.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.1945211 0.36242         -442.8320994  5.7763         -448.6083710  54.500  51.163   1.742 125.165
        Known (#1)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -443.1945211 0.36242        -442.8320994  5.7763        -448.6083710  54.500  51.163   1.742 125.165
   1     -448.6083710  2.1740        -446.4343612  3.3529        -449.7872410   9.763   7.599  19.962  10.921
   3     -449.7872410  4.8257        -444.9615041  4.7831        -449.7446477  15.678  13.792  15.617  13.959

 Number of TS in the path       =      3
 Number of cycles               =      2

 Elapsed time=                               526.25
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             39074 time=         287.96 %= 54.7
 OPTIM> # of energy+gradient+Hessian calls=       298 time=          88.42 %= 16.8
