
 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 05/24/2012 at 10:56:26
  [-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> 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
 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -535.3662400     RMS force=    0.9061237859E-06
 OPTIM> Final energy  =    -536.9382472     RMS force=    0.9826665831E-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=     31122.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.46     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 315 RMS= 0.0966 Dev= 1.44% S= 36.67 time= 5.70
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     575 steps. Energy=    -535.2457314       time=       1.42
 Minus side of path:                     558 steps. Energy=    -535.4379723       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2457314 0.96127         -534.2844599  1.1535         -535.4379723  17.374  16.847   2.895  36.966
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     6826.4    
 decide> The unconnected minima in the chain and their distances are:
     2       16.97     4     3       12.47     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0988 Dev= 0.33% S= 17.99 time= 1.76
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         61
 DNEB run yielded 1 true transition state(s) time=   6.21

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     612 steps. Energy=    -536.9382472       time=       1.51
 Minus side of path:                     617 steps. Energy=    -537.7197852       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.9382472 0.11427         -536.8239740 0.89581         -537.7197852   9.818   8.803   5.018  21.322
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1851 Dev= 0.05% S= 12.81 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   3.73

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     592 steps. Energy=    -534.9399987       time=       1.54
 Minus side of path:                     593 steps. Energy=    -535.2457314       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.9399987 0.74840E-01     -534.8651586 0.38057         -535.2457314   5.324   3.737   6.656  16.076
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     4714.1    
 decide> The unconnected minima in the chain and their distances are:
     5       13.74     4     6       12.85     1 
 

 tryconnect> 140-iteration DNEB run for minima 4_U and 5_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0961 Dev= 0.42% S= 14.25 time= 1.14
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.44

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     591 steps. Energy=    -535.4379723       time=       1.46
 Minus side of path:                     687 steps. Energy=    -537.7197852       time=       1.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.4379723 0.29773         -535.1402453  2.5795         -537.7197852  14.240  13.752   2.791  38.333
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1496 Dev= 0.14% S= 13.32 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.53

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     610 steps. Energy=    -534.9399987       time=       1.49
 Minus side of path:                     620 steps. Energy=    -535.3662400       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.9399987 0.84303         -534.0969668  1.2693         -535.3662400  14.235  12.855   4.013  26.666
        Known (#6)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -535.3662400  1.2693        -534.0969668 0.84303        -534.9399987  14.235  12.855   4.013  26.666
   3     -534.9399987 0.74840E-01    -534.8651586 0.38057        -535.2457314   5.324   3.737   6.656  16.076
   1     -535.2457314 0.96127        -534.2844599  1.1535        -535.4379723  17.374  16.847   2.895  36.966
   4     -535.4379723 0.29773        -535.1402453  2.5795        -537.7197852  14.240  13.752   2.791  38.333
   2     -537.7197852 0.89581        -536.8239740 0.11427        -536.9382472   9.818   8.803   5.018  21.322

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

 Elapsed time=                                51.66
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             14144 time=          28.36 %= 54.9
 OPTIM> # of energy+gradient+Hessian calls=       244 time=          13.47 %= 26.1
