
 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 11:58:40
  [-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 = 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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.9683128     RMS force=    0.9527730669E-06
 OPTIM> Final energy  =    -535.5515772     RMS force=    0.9861479562E-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=     6142.1    
 decide> The unconnected minima in the chain and their distances are:
     2       18.31     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.4005 Dev= 0.78% S= 22.90 time= 1.81
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  32.68
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     12284.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.31     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 805 RMS= 0.1355 Dev= 4.37% S= 28.16 time= 37.26
 Following    4 images are candidates for TS:    7   11   14   21  
 Converged to TS (number of iterations):        109
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         64
 Converged to TS (number of iterations):         19
 DNEB run yielded 3 true transition state(s) time=  43.18

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1058 steps. Energy=    -537.4643304       time=       2.96
 Minus side of path:                     632 steps. Energy=    -533.7204411       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.4643304  3.7443         -533.7200542 0.38685E-03     -533.7204411  15.939  15.650   2.593  41.268
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     636 steps. Energy=    -535.3587217       time=       1.59
 Minus side of path:                     680 steps. Energy=    -537.1728982       time=       1.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.3587217 0.41420         -534.9445230  2.2284         -537.1728982  15.902  12.135   7.805  13.709
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     629 steps. Energy=    -536.6372301       time=       1.59
 Minus side of path:                     622 steps. Energy=    -535.5515772       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.6372301  1.5630         -535.0742725 0.47730         -535.5515772   5.916   5.479  10.876   9.838
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     2184.6    
 decide> The unconnected minima in the chain and their distances are:
     7       11.85     5     6        3.60     3     4        7.81     1 
 

 tryconnect> 105-iteration DNEB run for minima 5_U and 7_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0878 Dev= 0.07% S= 12.01 time= 0.66
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.36

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     638 steps. Energy=    -536.5941373       time=       1.57
 Minus side of path:                     609 steps. Energy=    -535.3587217       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.5941373  1.3056         -535.2885066 0.70215E-01     -535.3587217  11.201  10.815   2.890  37.020
        *NEW* (Placed in 8)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.4007 Dev= 2.18% S= 4.17 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=   5.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     637 steps. Energy=    -537.1728982       time=       1.57
 Minus side of path:                     642 steps. Energy=    -537.0986173       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.1728982 0.30519         -536.8677058 0.23091         -537.0986173  12.661  11.578   2.394  44.694
        Known (#6)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0784 Dev= 0.08% S= 7.89 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.70

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     699 steps. Energy=    -533.9683128       time=       1.77
 Minus side of path:                     654 steps. Energy=    -533.7204411       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9683128 0.27733         -533.6909865 0.29455E-01     -533.7204411   8.276   7.808   5.535  19.332
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     108.67    
 decide> The unconnected minima in the chain and their distances are:
     7        2.49     8     6        3.60     3 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 8_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1655 Dev= 0.11% S= 2.49 time= 0.30
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.24

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     593 steps. Energy=    -536.6372301       time=       1.45
 Minus side of path:                     569 steps. Energy=    -536.5941373       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.6372301 0.49065E-01     -536.5881654 0.59719E-02     -536.5941373   2.497   2.488  10.302  10.387
        Known (#7)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 3_S and 6_F using 8 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 280 RMS= 0.0398 Dev= 5.09% S= 5.02 time= 4.57
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.38

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     636 steps. Energy=    -537.4643304       time=       1.59
 Minus side of path:                     639 steps. Energy=    -537.1728982       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.4643304  8.4076         -529.0567193  8.1162         -537.1728982   4.382   3.600  17.949   5.961
        Known (#3)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -533.9683128 0.27733        -533.6909865 0.29455E-01    -533.7204411   8.276   7.808   5.535  19.332
   1     -533.7204411 0.38685E-03    -533.7200542  3.7443        -537.4643304  15.939  15.650   2.593  41.268
   8     -537.4643304  8.4076        -529.0567193  8.1162        -537.1728982   4.382   3.600  17.949   5.961
   2     -537.1728982  2.2284        -534.9445230 0.41420        -535.3587217  15.902  12.135   7.805  13.709
   4     -535.3587217 0.70215E-01    -535.2885066  1.3056        -536.5941373  11.201  10.815   2.890  37.020
   7     -536.5941373 0.59719E-02    -536.5881654 0.49065E-01    -536.6372301   2.497   2.488  10.302  10.387
   3     -536.6372301  1.5630        -535.0742725 0.47730        -535.5515772   5.916   5.479  10.876   9.838

 Number of TS in the path       =      7
 Number of cycles               =      4

 Elapsed time=                               167.53
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42741 time=          85.05 %= 50.8
 OPTIM> # of energy+gradient+Hessian calls=       842 time=          45.46 %= 27.1
