
 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 12:00:01
  [-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=    -528.4878495     RMS force=    0.7909787521E-06
 OPTIM> Final energy  =    -531.1339872     RMS force=    0.9407065881E-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=     3699.6    
 decide> The unconnected minima in the chain and their distances are:
     2       15.47     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1997 Dev= 0.61% S= 16.47 time= 1.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         91
 DNEB run yielded 1 true transition state(s) time=   8.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     845 steps. Energy=    -534.4264545       time=       2.24
 Minus side of path:                     616 steps. Energy=    -528.4418681       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4264545  5.9988         -528.4276047 0.14263E-01     -528.4418681  12.584  12.043   3.291  32.511
        *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      2 steps with      2 missing connections, weight=     2960.6    
 decide> The unconnected minima in the chain and their distances are:
     2       14.34     4     4        2.21     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.5403 Dev= 0.49% S= 15.33 time= 1.16
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        180
 DNEB run yielded 1 true transition state(s) time=  16.81
 isnewts> transition state is the same as number        1 energy=     -528.4276046542
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     845 steps. Energy=    -534.4264545       time=       2.29
 Minus side of path:                     592 steps. Energy=    -528.4418681       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4264545  5.9988         -528.4276047 0.14263E-01     -528.4418681  12.577  12.035   3.307  32.356
        Known (#3)                                              Known (#4)
 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= 0.0312 Dev= 0.05% S= 2.22 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.85

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     637 steps. Energy=    -528.4418681       time=       1.61
 Minus side of path:                     648 steps. Energy=    -528.4878495       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.4418681 0.51131E-01     -528.3907370 0.97113E-01     -528.4878495   2.285   2.214   5.289  20.231
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4784.2    
 decide> The unconnected minima in the chain and their distances are:
     2       16.85     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1338 Dev= 0.43% S= 17.86 time= 1.80
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   8.05

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     584 steps. Energy=    -533.2932621       time=       1.44
 Minus side of path:                     706 steps. Energy=    -534.4264545       time=       1.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2932621 0.46936E-01     -533.2463264  1.1801         -534.4264545   7.097   6.273   6.971  15.350
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3434.1    
 decide> The unconnected minima in the chain and their distances are:
     2       15.09     5 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 5_S using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0989 Dev= 0.15% S= 15.84 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=   6.98

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     641 steps. Energy=    -531.7217860       time=       1.63
 Minus side of path:                     747 steps. Energy=    -533.2932621       time=       1.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7217860 0.36287         -531.3589207  1.9343         -533.2932621  15.071  13.326   4.822  22.190
        *NEW* (Placed in 6)                                     Known (#5)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     163.84    
 decide> The unconnected minima in the chain and their distances are:
     2        5.47     6 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0746 Dev= 0.14% S= 5.52 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.43

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     601 steps. Energy=    -531.1339872       time=       1.50
 Minus side of path:                     673 steps. Energy=    -531.7254312       time=       1.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.1339872 0.10546         -531.0285241 0.69691         -531.7254312   5.809   5.513   4.792  22.328
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=    0.33035    
 decide> The unconnected minima in the chain and their distances are:
     7        0.69     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 7_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0094 Dev= 0.04% S= 0.69 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.08

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     587 steps. Energy=    -531.7217860       time=       1.44
 Minus side of path:                     608 steps. Energy=    -531.7254312       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7217860 0.11530E-02     -531.7206330 0.47982E-02     -531.7254312   0.694   0.691  10.399  10.290
        Known (#6)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -528.4878495 0.97113E-01    -528.3907370 0.51131E-01    -528.4418681   2.285   2.214   5.289  20.231
   1     -528.4418681 0.14263E-01    -528.4276047  5.9988        -534.4264545  12.584  12.043   3.291  32.511
   4     -534.4264545  1.1801        -533.2463264 0.46936E-01    -533.2932621   7.097   6.273   6.971  15.350
   5     -533.2932621  1.9343        -531.3589207 0.36287        -531.7217860  15.071  13.326   4.822  22.190
   7     -531.7217860 0.11530E-02    -531.7206330 0.47982E-02    -531.7254312   0.694   0.691  10.399  10.290
   6     -531.7254312 0.69691        -531.0285241 0.10546        -531.1339872   5.809   5.513   4.792  22.328

 Number of TS in the path       =      6
 Number of cycles               =      6

 Elapsed time=                                79.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             17507 time=          35.31 %= 44.6
 OPTIM> # of energy+gradient+Hessian calls=       469 time=          25.72 %= 32.5
