
 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 17:42:40
  [-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=    -449.8827792     RMS force=    0.9257082896E-06
 OPTIM> Final energy  =    -450.3132511     RMS force=    0.8329637285E-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      55.53808980    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.14194E+06
 decide> The unconnected minima in the chain and their distances are:
     2       52.11     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=    15
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    729 fraction=    0.990000 images=     5 time=       1.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    754 steps, energy/image=    -421.4479921     RMS=1.942159588     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   55.20     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 560 RMS= 0.0351 Dev= 5.73% S= 62.17 time= 66.68
 Following    2 images are candidates for TS:    6   13  
 Converged to TS (number of iterations):        112
 Converged to TS (number of iterations):        141
 DNEB run yielded 2 true transition state(s) time= 149.69

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1314 steps. Energy=    -452.6427403       time=      16.43
 Minus side of path:                    1344 steps. Energy=    -453.9460560       time=      14.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.6427403 0.44366         -452.1990767  1.7470         -453.9460560  35.186  32.090   4.296  50.743
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    20   21 from     0.16842E-01 to     0.16922E-01 ref=     2.1008    
 checkperc> Increasing con cutoff atoms    20   22 from     0.10924     to     0.10926     ref=     3.2801    
 checkperc> Increasing con cutoff atoms    20   24 from     0.72508E-01 to     0.72598E-01 ref=     4.2650    
 checkperc> Increasing con cutoff atoms    20   25 from     0.11186     to     0.11192     ref=     5.2040    
 checkperc> Increasing con cutoff atoms    37   39 from     0.59469E-02 to     0.59726E-02 ref=     3.1447    
 checkperc> Increasing con cutoff atoms    41   50 from     0.18980E-01 to     0.19249E-01 ref=     2.1234    
 checkperc> Increasing con cutoff atoms    42   43 from     0.32284E-03 to     0.33514E-03 ref=     1.0929    
 checkperc> Increasing con cutoff atoms    54   74 from     0.39310E-02 to     0.39733E-02 ref=     1.5425    
 checkperc> Increasing con cutoff atoms    62   63 from     0.10452E-02 to     0.10536E-02 ref=     1.0152    
 checkperc> Increasing con cutoff atoms    64   66 from     0.78924E-03 to     0.79611E-03 ref=     2.1603    
 checkperc> Increasing con cutoff atoms   147  153 from     0.63031E-02 to     0.67674E-02 ref=     2.8162    
 checkperc> Increasing con cutoff atoms   147  154 from     0.92744E-02 to     0.99026E-02 ref=     3.8940    
 checkperc> Increasing con cutoff atoms    26   27 from     0.70775E-03 to     0.83060E-03 ref=     1.4034    
 checkperc> Increasing con cutoff atoms    36   37 from     0.14982E-02 to     0.15664E-02 ref=     1.2356    
 checkperc> Increasing con cutoff atoms   150  151 from     0.64561E-02 to     0.66626E-02 ref=     2.1640    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    2769 steps. Energy=    -452.8850823       time=      45.90
 Minus side of path:                    1364 steps. Energy=    -450.3132511       time=      14.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8850823  5.6108         -447.2742587  3.0390         -450.3132511 111.564  92.451   1.980 110.088
        *NEW* (Placed in 5)                                     Known (#2)
 checkperc> Increasing con cutoff atoms     1    8 from     0.14673E-01 to     0.14693E-01 ref=     2.7921    
 checkperc> Increasing con cutoff atoms     3    8 from     0.14377E-01 to     0.14405E-01 ref=     3.7261    
 checkperc> Increasing con cutoff atoms     4    5 from     0.51490E-02 to     0.51627E-02 ref=     2.0725    
 checkperc> Increasing con cutoff atoms     4    8 from     0.25250E-01 to     0.25289E-01 ref=     2.6324    
 checkperc> Increasing con cutoff atoms     4    9 from     0.15534E-01 to     0.15565E-01 ref=     3.7483    
 checkperc> Increasing con cutoff atoms     6    9 from     0.81570E-02 to     0.81622E-02 ref=     2.4361    
 checkperc> Increasing con cutoff atoms     8    9 from     0.87318E-03 to     0.87599E-03 ref=     1.7760    
 checkperc> Increasing con cutoff atoms     8   10 from     0.18629E-02 to     0.18651E-02 ref=     2.0609    
 checkperc> Increasing con cutoff atoms     9   12 from     0.12540E-01 to     0.12568E-01 ref=     2.7436    
 checkperc> Increasing con cutoff atoms    14   16 from     0.43117E-02 to     0.43136E-02 ref=     1.4752    
 checkperc> Increasing con cutoff atoms    16   37 from     0.78578E-02 to     0.79102E-02 ref=     2.4213    
 checkperc> Increasing con cutoff atoms    21   32 from     0.30178E-02 to     0.31233E-02 ref=     4.7967    
 checkperc> Increasing con cutoff atoms    31   33 from     0.64126E-03 to     0.65491E-03 ref=     1.4087    
 checkperc> Increasing con cutoff atoms    31   35 from     0.15432E-02 to     0.15703E-02 ref=     2.4575    
 checkperc> Increasing con cutoff atoms    32   33 from     0.14846E-02 to     0.16017E-02 ref=     2.1603    
 checkperc> Increasing con cutoff atoms    32   35 from     0.19060E-02 to     0.20134E-02 ref=     3.4318    
 checkperc> Increasing con cutoff atoms   110  111 from     0.24140E-02 to     0.26920E-02 ref=     1.2320    
 checkperc> Increasing con cutoff atoms   110  115 from     0.77405E-01 to     0.91315E-01 ref=     2.6782    
 checkperc> Increasing con cutoff atoms   111  112 from     0.84622E-02 to     0.91279E-02 ref=     2.2532    
 checkperc> Increasing con cutoff atoms   111  113 from     0.88887E-02 to     0.10936E-01 ref=     3.1349    
 checkperc> Increasing con cutoff atoms   113  115 from     0.70851E-01 to     0.10763     ref=     2.9332    
 checkperc> Increasing con cutoff atoms   122  131 from     0.11163     to     0.11288     ref=     2.7291    
 checkperc> Increasing con cutoff atoms   126  131 from     0.96992E-01 to     0.97786E-01 ref=     2.4705    
 checkperc> Increasing con cutoff atoms   127  129 from     0.91886E-01 to     0.93345E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms   127  130 from     0.10070     to     0.10214     ref=     2.4467    
 checkperc> Increasing con cutoff atoms   130  131 from     0.10381E-01 to     0.10596E-01 ref=     1.6379    
 checkperc> Increasing con cutoff atoms   132  133 from     0.19874E-02 to     0.20310E-02 ref=     1.2342    
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     93206.    
 decide> The unconnected minima in the chain and their distances are:
     2       12.03     4     3       45.01     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=   205
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     86 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    111 steps, energy/image=    -444.6114330     RMS=.3814433613     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   16.37     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2587 Dev= 0.85% S= 14.78 time= 4.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=  21.43

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1242 steps. Energy=    -450.3132511       time=      13.39
 Minus side of path:                    1249 steps. Energy=    -453.9460560       time=      13.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3132511  2.4320         -447.8812133  6.0648         -453.9460560  14.057  12.052  18.370  11.867
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=    31
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    321 fraction=    0.990000 images=     4 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    346 steps, energy/image=    -435.1234889     RMS=1.179898021     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   46.51     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0121 Dev= 0.33% S= 47.66 time= 43.97
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  20.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1228 steps. Energy=    -449.8827792       time=      12.60
 Minus side of path:                    1381 steps. Energy=    -452.6427403       time=      14.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.8827792 0.72148E-01     -449.8106317  2.8321         -452.6427403  46.314  45.082   2.642  82.504
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -449.8827792 0.72148E-01    -449.8106317  2.8321        -452.6427403  46.314  45.082   2.642  82.504
   1     -452.6427403 0.44366        -452.1990767  1.7470        -453.9460560  35.186  32.090   4.296  50.743
   3     -453.9460560  6.0648        -447.8812133  2.4320        -450.3132511  14.057  12.052  18.370  11.867

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

 Elapsed time=                               459.33
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             33213 time=         245.35 %= 53.4
 OPTIM> # of energy+gradient+Hessian calls=       293 time=          86.98 %= 18.9
