
 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 05/25/2012 at 12:51:26
  [-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 = 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>> 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=    -447.6268301     RMS force=    0.9384062946E-06
 OPTIM> Final energy  =    -449.3686196     RMS force=    0.9156143465E-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=    0.11272E+06
 decide> The unconnected minima in the chain and their distances are:
     2       48.31     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 2_F using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 490 RMS= 0.1268 Dev= 5.81% S= 53.25 time= 51.10
 Following    1 images are candidates for TS:    7  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  60.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1282 steps. Energy=    -449.3686196       time=      13.63
 Minus side of path:                    1308 steps. Energy=    -450.2634452       time=      13.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3686196 0.54259E-01     -449.3143610 0.94908         -450.2634452  13.531  12.606   4.136  52.709
        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=    0.11378E+06
 decide> The unconnected minima in the chain and their distances are:
     3       48.46     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 3_F using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 490 RMS= 0.0732 Dev= 6.86% S= 54.84 time= 51.19
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        162
 DNEB run yielded 1 true transition state(s) time=  82.41

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1296 steps. Energy=    -448.6323677       time=      13.42
 Minus side of path:                    1297 steps. Energy=    -447.7721702       time=      13.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6323677 0.93827         -447.6940976 0.78073E-01     -447.7721702  13.839  12.347   4.092  53.277
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     61595.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     5     4       38.00     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 175 RMS= 0.4192 Dev= 2.16% S= 20.63 time= 6.59
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         84
 DNEB run yielded 1 true transition state(s) time=  50.62

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1431 steps. Energy=    -449.1179824       time=      15.59
 Minus side of path:                    1329 steps. Energy=    -449.3686196       time=      13.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.1179824  1.0269         -448.0911187  1.2775         -449.3686196  35.745  34.995   1.693 128.733
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_U using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 385 RMS= 0.0261 Dev= 0.43% S= 39.33 time= 31.63
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  28.18

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1346 steps. Energy=    -448.2254512       time=      14.19
 Minus side of path:                    1316 steps. Energy=    -447.6268301       time=      13.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2254512 0.80157         -447.4238804 0.20295         -447.6268301  17.418  11.874   6.153  35.430
        *NEW* (Placed in 7)                                     Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     47247.    
 decide> The unconnected minima in the chain and their distances are:
     3       18.91     4     4       34.34     7 
 

 tryconnect> 175-iteration DNEB run for minima 3_F and 4_U using 5 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 175 RMS= 1.8373 Dev= 2.10% S= 20.77 time= 6.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  42.84

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1321 steps. Energy=    -450.2634452       time=      13.85
 Minus side of path:                    1367 steps. Energy=    -449.8326857       time=      14.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2634452  1.2482         -449.0152383 0.81745         -449.8326857  32.820  32.057   1.741 125.209
        Known (#3)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 4_U and 7_S using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 350 RMS= 0.0211 Dev= 0.12% S= 34.88 time= 26.22
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=  33.20

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1302 steps. Energy=    -448.2254512       time=      13.51
 Minus side of path:                    1380 steps. Energy=    -448.6323677       time=      14.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2254512 0.22569         -447.9997593 0.63261         -448.6323677  37.226  34.474   1.770 123.163
        Known (#7)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     9366.0    
 decide> The unconnected minima in the chain and their distances are:
     3       21.08     5 
 

 tryconnect> 210-iteration DNEB run for minima 3_F and 5_S using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 210 RMS= 0.1694 Dev= 1.82% S= 23.19 time= 9.48
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=  39.94
 isnewts> transition state is the same as number        1 energy=     -449.3143609538
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1303 steps. Energy=    -449.3686196       time=      13.51
 Minus side of path:                    1335 steps. Energy=    -450.2634452       time=      14.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3686196 0.54259E-01     -449.3143610 0.94908         -450.2634452  13.531  12.606   4.138  52.683
        Known (#2)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     13452.    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     5 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_S using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.5621229993    
 Double-ended search iterations= 805 RMS= 0.0224 Dev= 4.88% S= 28.96 time= 137.43
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  35.31

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1348 steps. Energy=    -447.6268301       time=      14.45
 Minus side of path:                    1605 steps. Energy=    -450.2634452       time=      19.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6268301  5.3526         -442.2742282  7.9892         -450.2634452  50.726  48.464   1.782 122.315
        Known (#1)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -447.6268301  5.3526        -442.2742282  7.9892        -450.2634452  50.726  48.464   1.782 122.315
   1     -450.2634452 0.94908        -449.3143610 0.54259E-01    -449.3686196  13.531  12.606   4.136  52.709

 Number of TS in the path       =      2
 Number of cycles               =      6

 Elapsed time=                               922.71
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             76268 time=         561.98 %= 60.9
 OPTIM> # of energy+gradient+Hessian calls=       610 time=         166.90 %= 18.1
