
 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 05/28/2012 at 09:27:06
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 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=    17
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>  321 Cartesian coordinates will be optimised for  107 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=    -529.0629643     RMS force=    0.9039884495E-06
 OPTIM> Final energy  =    -533.9808646     RMS force=    0.9646218815E-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      79.25743915    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     3578.7    
 decide> The unconnected minima in the chain and their distances are:
     2       15.22     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=    80
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    336 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    361 steps, energy/image=    -506.3959635     RMS=1.885691011     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   21.93     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      1.420456823    
 Double-ended search iterations= 210 RMS= 0.3626 Dev= 0.97% S= 22.45 time= 2.57
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.22

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     682 steps. Energy=    -529.0629643       time=       1.86
 Minus side of path:                     732 steps. Energy=    -533.9808646       time=       1.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.0629643  3.1886         -525.8743143  8.1066         -533.9808646  17.377  12.552   4.825  22.177
        Known (#1)                                              *NEW* (Placed in 3)
 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=     1006.0    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     3 
 

 checkpair> Energies of the minima in the pair     2    3 are the same - checking distance ...

 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=    99
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    311 fraction=    0.990000 images=     1 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    336 steps, energy/image=     11162.40513     RMS=6841.606558     images=   1
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   18.20     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 0.3516 Dev= 1.30% S= 17.10 time= 1.79
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.67

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     645 steps. Energy=    -533.1882481       time=       1.67
 Minus side of path:                     672 steps. Energy=    -533.9808646       time=       1.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.1882481  5.5890         -527.5992370  6.3816         -533.9808646  22.332  11.113  12.763   8.384
        *NEW* (Placed in 4)                                     Known (#3)
 checkperc> Increasing con cutoff atoms     9   10 from     0.49019E-02 to     0.51197E-02 ref=     2.2523    
 checkperc> Increasing con cutoff atoms    42   44 from     0.10011E-02 to     0.11163E-02 ref=     1.0907    
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     135.73    
 decide> The unconnected minima in the chain and their distances are:
     2        5.13     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=   103
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     28 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     53 steps, energy/image=    -525.5357814     RMS=.7942663802     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   5.668     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3258 Dev= 1.88% S= 5.67 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   8.27

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     616 steps. Energy=    -533.9808646       time=       1.50
 Minus side of path:                     612 steps. Energy=    -532.2000673       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9808646  2.4532         -531.5276790 0.67239         -532.2000673  12.209  10.831   7.734  13.835
        Known (#2)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    74   88 from     0.38325E-01 to     0.40676E-01 ref=     3.8815    
 checkperc> Increasing con cutoff atoms    92   98 from     0.53794E-01 to     0.60185E-01 ref=     4.7852    
 checkperc> Increasing con cutoff atoms    92   99 from     0.62400E-01 to     0.69683E-01 ref=     6.1212    
 checkperc> Increasing con cutoff atoms    99  101 from     0.96844E-02 to     0.11764E-01 ref=     2.4050    
 checkperc> Increasing con cutoff atoms    99  102 from     0.18986E-01 to     0.22759E-01 ref=     2.6446    
 checkperc> Increasing con cutoff atoms    99  103 from     0.78605E-02 to     0.91410E-02 ref=     3.6880    
 checkperc> Increasing con cutoff atoms    99  104 from     0.10945E-01 to     0.12708E-01 ref=     4.5631    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     271.47    
 decide> The unconnected minima in the chain and their distances are:
     2        5.13     4 
 

 tryconnect> Interpolation for minima 2_F and 4_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=   103
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     24 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     49 steps, energy/image=    -528.1874169     RMS=.5212837933     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   6.066     Attempts, images and iterations=     1    13   455
 lbfgs> Final DNEB force constant      37.33456322    
 Double-ended search iterations= 455 RMS= 0.3527 Dev= 4.89% S= 6.31 time= 12.06
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.42

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     606 steps. Energy=    -533.9808646       time=       1.48
 Minus side of path:                     610 steps. Energy=    -533.1882481       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9808646  8.8610         -525.1198393  8.0684         -533.1882481   5.490   5.135  14.540   7.359
        Known (#2)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -529.0629643  3.1886        -525.8743143  8.1066        -533.9808646  17.377  12.552   4.825  22.177
   2     -533.9808646  6.3816        -527.5992370  5.5890        -533.1882481  22.332  11.113  12.763   8.384
   4     -533.1882481  8.0684        -525.1198393  8.8610        -533.9808646   5.490   5.135  14.540   7.359

 Number of TS in the path       =      3
 Number of cycles               =      4

 Elapsed time=                                51.23
 OPTIM> # of energy calls=                          8 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             16731 time=          33.39 %= 65.2
 OPTIM> # of energy+gradient+Hessian calls=       170 time=           9.20 %= 17.9
