
 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 05/23/2012 at 21:33:02
  [-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> 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
 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> 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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -447.4397567     RMS force=    0.8619167892E-06
 OPTIM> Final energy  =    -450.3205708     RMS force=    0.9503196461E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.10935E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.82     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 490 RMS= 0.0835 Dev= 5.41% S= 60.36 time= 52.30
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        105
 DNEB run yielded 1 true transition state(s) time=  74.47

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1554 steps. Energy=    -450.3205708       time=      19.89
 Minus side of path:                    1466 steps. Energy=    -449.5445889       time=      18.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3205708  8.0431         -442.2774417  7.2671         -449.5445889  56.495  34.219   3.065  71.119
        Known (#2)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.17612E+06
 decide> The unconnected minima in the chain and their distances are:
     3       56.05     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 3_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0360 Dev= 3.56% S= 62.55 time= 68.34
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  30.06

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1387 steps. Energy=    -449.5718243       time=      15.30
 Minus side of path:                    1360 steps. Energy=    -447.4397567       time=      14.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.5718243  2.8294         -446.7424583 0.69730         -447.4397567  45.966  44.308   1.734 125.718
        *NEW* (Placed in 4)                                     Known (#1)
 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      2 steps with      1 missing connections, weight=     4524.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.54     4 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 1.0094 Dev= 1.26% S= 18.64 time= 4.43
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=  56.14
 isnewts> transition state is the same as number        1 energy=     -442.2774416942
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1580 steps. Energy=    -450.3205708       time=      17.96
 Minus side of path:                    1476 steps. Energy=    -449.5445889       time=      16.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3205708  8.0431         -442.2774417  7.2671         -449.5445889  56.508  34.175   3.069  71.038
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     9048.4    
 decide> The unconnected minima in the chain and their distances are:
     2       16.54     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 805 RMS= 0.0621 Dev= 4.71% S= 36.73 time= 137.54
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  42.57
 isnewts> transition state is the same as number        1 energy=     -442.2774416934
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     12849.    
 decide> The unconnected minima in the chain and their distances are:
     3       23.42     4 
 

 tryconnect> 245-iteration DNEB run for minima 3_F and 4_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0701 Dev= 0.18% S= 24.09 time= 13.18
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=  44.35

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1277 steps. Energy=    -449.5445889       time=      15.54
 Minus side of path:                    1328 steps. Energy=    -449.5718243       time=      16.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.5445889 0.54720         -448.9973916 0.57443         -449.5718243  25.308  23.430   3.414  63.849
        Known (#3)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -447.4397567 0.69730        -446.7424583  2.8294        -449.5718243  45.966  44.308   1.734 125.718
   4     -449.5718243 0.57443        -448.9973916 0.54720        -449.5445889  25.308  23.430   3.414  63.849
   1     -449.5445889  7.2671        -442.2774417  8.0431        -450.3205708  56.495  34.219   3.065  71.119

 Number of TS in the path       =      3
 Number of cycles               =      5

 Elapsed time=                               658.12
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             55158 time=         410.81 %= 62.4
 OPTIM> # of energy+gradient+Hessian calls=       370 time=         109.19 %= 16.6
