
 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 21:20:26
  [-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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -459.2275153     RMS force=    0.9774241981E-06
 OPTIM> Final energy  =    -452.2692150     RMS force=    0.7988522514E-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=    0.12866E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.48     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 525 RMS= 0.0633 Dev= 1.26% S= 61.62 time= 58.27
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=  32.00

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1242 steps. Energy=    -452.2614211       time=      12.71
 Minus side of path:                    1407 steps. Energy=    -452.3550666       time=      15.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.2614211 0.18421         -452.0772070 0.27786         -452.3550666  15.693  13.334   3.700  58.923
        *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=     90139.    
 decide> The unconnected minima in the chain and their distances are:
     2        9.80     4     3       44.68     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0746 Dev= 0.01% S= 9.83 time= 1.33
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  24.62

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1170 steps. Energy=    -452.4073071       time=      11.51
 Minus side of path:                    1141 steps. Energy=    -452.2692150       time=      11.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4073071 0.14376         -452.2635457 0.56693E-02     -452.2692150   8.453   8.363   6.750  32.297
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 455-iteration DNEB run for minima 1_S and 3_U using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6832640190    
 Double-ended search iterations= 455 RMS= 0.1258 Dev= 2.70% S= 52.92 time= 43.69
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):        164
 DNEB run yielded 1 true transition state(s) time=  86.86

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1221 steps. Energy=    -452.5185169       time=      12.29
 Minus side of path:                    1490 steps. Energy=    -456.2424329       time=      16.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.5185169 0.45509E-01     -452.4730075  3.7694         -456.2424329  32.277  28.390   3.475  62.736
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     21684.    
 decide> The unconnected minima in the chain and their distances are:
     5        3.13     4     3       18.92     6     7       24.60     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0110 Dev= 0.17% S= 3.14 time= 1.32
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=  17.22

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1169 steps. Energy=    -452.4073071       time=      11.62
 Minus side of path:                    1129 steps. Energy=    -452.3550666       time=      10.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4073071 0.60329E-01     -452.3469786 0.80880E-02     -452.3550666   3.143   3.134   3.991  54.622
        Known (#5)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0351 Dev= 0.06% S= 19.12 time= 6.83
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=  28.52
 isnewts> transition state is the same as number        1 energy=     -452.0772069722
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1217 steps. Energy=    -452.2614211       time=      12.17
 Minus side of path:                    1383 steps. Energy=    -452.3550666       time=      14.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.2614211 0.18421         -452.0772070 0.27786         -452.3550666  15.693  13.334   3.699  58.939
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0669 Dev= 0.27% S= 25.26 time= 13.15
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  23.34

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1171 steps. Energy=    -456.2424329       time=      11.53
 Minus side of path:                    1257 steps. Energy=    -458.5342116       time=      12.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.2424329 0.53124E-01     -456.1893086  2.3449         -458.5342116  18.938  18.014   1.396 156.199
        Known (#7)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     8327.9    
 decide> The unconnected minima in the chain and their distances are:
     2       19.21     6     8       10.73     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 6_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0721 Dev= 0.02% S= 19.30 time= 6.83
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  41.86

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1242 steps. Energy=    -452.2692150       time=      12.50
 Minus side of path:                    1241 steps. Energy=    -452.2250396       time=      12.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.2692150 0.13698         -452.1322309 0.92809E-01     -452.2250396  14.895  14.656   1.673 130.274
        Known (#2)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1095 Dev= 0.03% S= 10.81 time= 2.65
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=  21.40

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1112 steps. Energy=    -458.5342116       time=      10.75
 Minus side of path:                    1225 steps. Energy=    -459.2275153       time=      12.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.5342116 0.28586E-01     -458.5056256 0.72189         -459.2275153  11.626  10.730   3.595  60.648
        Known (#8)                                              Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     818.69    
 decide> The unconnected minima in the chain and their distances are:
     9        9.35     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0593 Dev= 0.01% S= 9.36 time= 1.32
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  23.80

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1196 steps. Energy=    -452.2250396       time=      11.84
 Minus side of path:                    1228 steps. Energy=    -452.5185169       time=      12.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.2250396 0.14073E-02     -452.2236323 0.29488         -452.5185169   9.463   9.356   2.587  84.264
        Known (#9)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -459.2275153 0.72189        -458.5056256 0.28586E-01    -458.5342116  11.626  10.730   3.595  60.648
   6     -458.5342116  2.3449        -456.1893086 0.53124E-01    -456.2424329  18.938  18.014   1.396 156.199
   3     -456.2424329  3.7694        -452.4730075 0.45509E-01    -452.5185169  32.277  28.390   3.475  62.736
   9     -452.5185169 0.29488        -452.2236323 0.14073E-02    -452.2250396   9.463   9.356   2.587  84.264
   7     -452.2250396 0.92809E-01    -452.1322309 0.13698        -452.2692150  14.895  14.656   1.673 130.274

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

 Elapsed time=                               661.00
 OPTIM> # of energy calls=                        108 time=           0.80 %=  0.1
 OPTIM> # of energy+gradient calls=             51274 time=         379.23 %= 57.4
 OPTIM> # of energy+gradient+Hessian calls=       453 time=         125.87 %= 19.0
