
 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 17:42:25
  [-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=    -446.5430051     RMS force=    0.8750426765E-06
 OPTIM> Final energy  =    -447.5328331     RMS force=    0.9090014710E-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      37.66737153    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     12729.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.31     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   118
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    201 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    226 steps, energy/image=    -396.9258984     RMS=23.61061699     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   30.91     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.4175 Dev= 2.95% S= 32.03 time= 21.19
 Following    2 images are candidates for TS:    2    6  
 Converged to TS (number of iterations):         28
 Converged to TS (number of iterations):         89
 DNEB run yielded 2 true transition state(s) time=  80.21

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1311 steps. Energy=    -446.9477859       time=      15.51
 Minus side of path:                    1278 steps. Energy=    -446.5430051       time=      14.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.9477859 0.73097         -446.2168135 0.32619         -446.5430051  13.666  13.567   3.557  61.283
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1613 steps. Energy=    -447.6633929       time=      21.70
 Minus side of path:                    1474 steps. Energy=    -446.9374024       time=      20.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6633929  7.9942         -439.6691888  7.2682         -446.9374024  56.904  34.307   3.042  71.653
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 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=     2252.0    
 decide> The unconnected minima in the chain and their distances are:
     2        3.18     4     5       13.03     1 
 

 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=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     19 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     44 steps, energy/image=    -442.8511302     RMS=.9392876478     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   11.46     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 2.1944 Dev= 8.32% S= 6.52 time= 2.40
 Following    2 images are candidates for TS:    1    3  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         56
 Converged to TS (number of iterations):         18
 DNEB run yielded 2 true transition state(s) time=  68.64

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1444 steps. Energy=    -449.0251467       time=      16.89
 Minus side of path:                    1281 steps. Energy=    -447.5328331       time=      13.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0251467  1.5732         -447.4518990 0.80934E-01     -447.5328331  36.965  34.806   2.700  80.738
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1287 steps. Energy=    -447.6633929       time=      13.42
 Minus side of path:                    1285 steps. Energy=    -447.5328330       time=      13.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6633929 0.89422         -446.7691716 0.76366         -447.5328330   3.286   3.182  16.497  13.215
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 1_S 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=   178
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     41 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     66 steps, energy/image=    -437.2337960     RMS=3.404852957     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   18.18     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 175 RMS= 0.0354 Dev= 1.67% S= 13.23 time= 6.56
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=  35.69

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1334 steps. Energy=    -446.9374024       time=      15.28
 Minus side of path:                    1302 steps. Energy=    -446.5430051       time=      15.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.9374024 0.95186         -445.9855388 0.55747         -446.5430051  25.352  13.146   4.706  46.325
        Known (#5)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -446.5430051 0.55747        -445.9855388 0.95186        -446.9374024  25.352  13.146   4.706  46.325
   2     -446.9374024  7.2682        -439.6691888  7.9942        -447.6633929  56.904  34.307   3.042  71.653
   4     -447.6633929 0.89422        -446.7691716 0.76366        -447.5328331   3.286   3.182  16.497  13.215

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

 Elapsed time=                               378.82
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             24711 time=         183.97 %= 48.6
 OPTIM> # of energy+gradient+Hessian calls=       239 time=          68.91 %= 18.2
