
 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 22:14:22
  [-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=    -448.9859078     RMS force=    0.9301812816E-06
 OPTIM> Final energy  =    -449.3888234     RMS force=    0.9547965827E-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

 checkperc> Increasing con cutoff atoms   123  125 from     0.16405E-01 to     0.18509E-01 ref=     2.1548    
 checkperc> Increasing con cutoff atoms   135  136 from     0.13741E-01 to     0.14643E-01 ref=     2.1292    
 checkperc> Increasing con cutoff atoms   156  157 from     0.16140E-02 to     0.17979E-02 ref=     1.2356    
 checkperc> Increasing con cutoff atoms   157  159 from     0.11180E-01 to     0.14473E-01 ref=     3.1416    
 checkperc> Increasing con cutoff atoms   160  163 from     0.98671E-02 to     0.12977E-01 ref=     2.1599    
 checkperc> Increasing con cutoff atoms   164  166 from     0.21711E-03 to     0.23774E-03 ref=     1.0905    
 checkperc> Increasing con cutoff atoms   194  195 from     0.21219E-02 to     0.22235E-02 ref=     1.2354    
 checkperc> Increasing con cutoff atoms   198  199 from     0.13585E-02 to     0.18496E-02 ref=     1.0890    
 initialise> Interpolation metric value for minima 1 and 2 is      21.02803989    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     7294.1    
 decide> The unconnected minima in the chain and their distances are:
     2       19.37     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=   158
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    104 fraction=    0.990000 images=     4 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    129 steps, energy/image=    -389.3904880     RMS=9.436963463     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   36.36     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant      1.726574146    
 Double-ended search iterations= 350 RMS= 0.1005 Dev= 1.80% S= 22.89 time= 26.40
 Following    2 images are candidates for TS:    2    6  
 Converged to TS (number of iterations):         46
 Converged to TS (number of iterations):         59
 DNEB run yielded 2 true transition state(s) time=  76.69

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1291 steps. Energy=    -448.9859078       time=      15.56
 Minus side of path:                    1392 steps. Energy=    -452.3333083       time=      17.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.9859078 0.24773         -448.7381762  3.5951         -452.3333083  24.766  21.689   2.901  75.138
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   112  115 from     0.17332E-01 to     0.18233E-01 ref=     2.0957    
 checkperc> Increasing con cutoff atoms   122  123 from     0.17373E-02 to     0.22384E-02 ref=     1.0905    
 checkperc> Increasing con cutoff atoms   122  124 from     0.19658E-02 to     0.35786E-02 ref=     1.0903    
 checkperc> Increasing con cutoff atoms   128  131 from     0.53778E-02 to     0.54407E-02 ref=     1.0159    
 checkperc> Increasing con cutoff atoms   135  136 from     0.14643E-01 to     0.24104E-01 ref=     2.1292    
 checkperc> Increasing con cutoff atoms   142  151 from     0.35066E-02 to     0.41867E-02 ref=     4.6342    
 checkperc> Increasing con cutoff atoms   149  152 from     0.44230E-02 to     0.46758E-02 ref=     2.1595    
 checkperc> Increasing con cutoff atoms   149  153 from     0.18695E-02 to     0.21922E-02 ref=     2.4442    
 checkperc> Increasing con cutoff atoms   160  163 from     0.12977E-01 to     0.13710E-01 ref=     2.1599    
 checkperc> Increasing con cutoff atoms   160  174 from     0.27310E-01 to     0.89885E-01 ref=     3.8522    
 checkperc> Increasing con cutoff atoms   170  174 from     0.29723E-01 to     0.41982E-01 ref=     2.4987    
 checkperc> Increasing con cutoff atoms   172  174 from     0.76110E-02 to     0.77754E-02 ref=     1.4704    
 checkperc> Increasing con cutoff atoms   172  194 from     0.44311E-01 to     0.54901E-01 ref=     2.5031    
 checkperc> Increasing con cutoff atoms   175  194 from     0.24970E-01 to     0.26871E-01 ref=     2.1308    
 checkperc> Increasing con cutoff atoms   196  198 from     0.38283E-02 to     0.41167E-02 ref=     1.4779    
 checkperc> Increasing con cutoff atoms   198  199 from     0.18496E-02 to     0.32245E-02 ref=     1.0890    
 checkperc> Increasing con cutoff atoms   198  203 from     0.44535E-01 to     0.47272E-01 ref=     2.5984    
 checkperc> Increasing con cutoff atoms   203  205 from     0.21423E-02 to     0.21536E-02 ref=     1.0892    
 checkperc> Increasing con cutoff atoms   216  217 from     0.98161E-03 to     0.11185E-02 ref=     1.2533    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1364 steps. Energy=    -449.3888234       time=      15.35
 Minus side of path:                    1413 steps. Energy=    -453.9860184       time=      15.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3888234  4.4733         -444.9155110  9.0705         -453.9860184  37.965  32.444   3.894  55.980
        Known (#2)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   125  131 from     0.92365E-02 to     0.11523E-01 ref=     2.0830    
 checkperc> Increasing con cutoff atoms   127  131 from     0.94113E-02 to     0.12811E-01 ref=     2.9751    
 checkperc> Increasing con cutoff atoms   128  131 from     0.54407E-02 to     0.56010E-02 ref=     1.0159    
 checkperc> Increasing con cutoff atoms   134  156 from     0.37548E-01 to     0.38520E-01 ref=     2.5022    
 checkperc> Increasing con cutoff atoms   136  158 from     0.32825E-01 to     0.34661E-01 ref=     2.4679    
 checkperc> Increasing con cutoff atoms   136  159 from     0.68722E-01 to     0.71465E-01 ref=     2.5628    
 checkperc> Increasing con cutoff atoms   160  162 from     0.70023E-02 to     0.76299E-02 ref=     1.5411    
 checkperc> Increasing con cutoff atoms   180  188 from     0.35120E-02 to     0.37721E-02 ref=     5.6712    
 checkperc> Increasing con cutoff atoms   181  188 from     0.55296E-02 to     0.56062E-02 ref=     6.7220    
 checkperc> Increasing con cutoff atoms   196  198 from     0.41167E-02 to     0.46441E-02 ref=     1.4779    
 checkperc> Increasing con cutoff atoms   196  200 from     0.30611E-01 to     0.32595E-01 ref=     2.4860    
 checkperc> Increasing con cutoff atoms   198  199 from     0.32245E-02 to     0.41914E-02 ref=     1.0890    
 checkperc> Increasing con cutoff atoms   198  200 from     0.37218E-02 to     0.39950E-02 ref=     1.5442    
 checkperc> Increasing con cutoff atoms   198  216 from     0.41450E-02 to     0.49113E-02 ref=     1.5392    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1508.5    
 decide> The unconnected minima in the chain and their distances are:
     4       11.46     3 
 

 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=   175
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     44 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     69 steps, energy/image=    -443.2898782     RMS=4.037483518     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   17.34     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 175 RMS= 0.3718 Dev= 1.39% S= 11.58 time= 6.61
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  22.85

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1279 steps. Energy=    -452.3333083       time=      13.44
 Minus side of path:                    1311 steps. Energy=    -453.9860184       time=      13.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.3333083 0.19228E-01     -452.3140804  1.6719         -453.9860184  12.433  11.458   2.834  76.913
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -448.9859078 0.24773        -448.7381762  3.5951        -452.3333083  24.766  21.689   2.901  75.138
   3     -452.3333083 0.19228E-01    -452.3140804  1.6719        -453.9860184  12.433  11.458   2.834  76.913
   2     -453.9860184  9.0705        -444.9155110  4.4733        -449.3888234  37.965  32.444   3.894  55.980

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

 Elapsed time=                               225.75
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             16582 time=         123.86 %= 54.9
 OPTIM> # of energy+gradient+Hessian calls=       127 time=          36.33 %= 16.1
