
 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 21:44:35
  [-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=    -453.7577854     RMS force=    0.9929389878E-06
 OPTIM> Final energy  =    -451.2610977     RMS force=    0.9648242216E-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=     22904.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.40     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 280 RMS= 0.1632 Dev= 2.03% S= 38.07 time= 17.10
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         83
 DNEB run yielded 1 true transition state(s) time=  49.74

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1314 steps. Energy=    -450.3135112       time=      16.02
 Minus side of path:                    1231 steps. Energy=    -451.0524838       time=      15.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3135112  2.3577         -447.9557643  3.0967         -451.0524838  26.161  21.310   6.604  33.012
        *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=     20139.    
 decide> The unconnected minima in the chain and their distances are:
     2       16.19     4     4       25.14     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= 0.0765 Dev= 0.08% S= 16.44 time= 4.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=  40.24

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1175 steps. Energy=    -451.0524838       time=      11.85
 Minus side of path:                    1197 steps. Energy=    -451.1732957       time=      11.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0524838 0.80510         -450.2473800 0.92592         -451.1732957  16.330  15.176   2.218  98.298
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 245 RMS= 1.4849 Dev= 1.25% S= 31.46 time= 12.89
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        188
 DNEB run yielded 1 true transition state(s) time=  97.16

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1214 steps. Energy=    -451.8584343       time=      12.17
 Minus side of path:                    1217 steps. Energy=    -451.8019401       time=      12.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.8584343 0.79248         -451.0659591 0.73598         -451.8019401  23.718  22.260   2.075 105.081
        *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      5 steps with      3 missing connections, weight=     20686.    
 decide> The unconnected minima in the chain and their distances are:
     2       10.33     5     3       15.38     7     7       25.17     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1079 Dev= 0.07% S= 10.37 time= 2.42
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  22.14

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1185 steps. Energy=    -451.1732957       time=      11.85
 Minus side of path:                    1241 steps. Energy=    -451.2610977       time=      12.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.1732957 0.82892         -450.3443771 0.91672         -451.2610977  10.771  10.332   2.838  76.811
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 140-iteration DNEB run for minima 3_F and 7_U using 4 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1623 Dev= 0.34% S= 16.03 time= 4.25
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=  37.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1235 steps. Energy=    -450.2940768       time=      12.44
 Minus side of path:                    1197 steps. Energy=    -450.3135112       time=      11.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2940768 0.86818         -449.4258949 0.88762         -450.3135112  13.467  12.100   8.166  26.697
        *NEW* (Placed in 8)                                     Known (#3)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_U using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.4574 Dev= 0.57% S= 26.42 time= 12.92
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  33.13

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1245 steps. Energy=    -451.8019401       time=      12.66
 Minus side of path:                    1260 steps. Energy=    -453.7577854       time=      12.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.8019401  1.1895         -450.6124809  3.1453         -453.7577854  29.380  25.173   4.141  52.645
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     985.47    
 decide> The unconnected minima in the chain and their distances are:
     8        9.95     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2884 Dev= 0.01% S= 10.02 time= 1.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=  25.28

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1227 steps. Energy=    -451.8019401       time=      12.38
 Minus side of path:                    1226 steps. Energy=    -450.2940768       time=      12.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.8019401  1.8241         -449.9778480 0.31623         -450.2940768  12.645   9.952   6.083  35.840
        Known (#7)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -453.7577854  3.1453        -450.6124809  1.1895        -451.8019401  29.380  25.173   4.141  52.645
   7     -451.8019401  1.8241        -449.9778480 0.31623        -450.2940768  12.645   9.952   6.083  35.840
   5     -450.2940768 0.86818        -449.4258949 0.88762        -450.3135112  13.467  12.100   8.166  26.697
   1     -450.3135112  2.3577        -447.9557643  3.0967        -451.0524838  26.161  21.310   6.604  33.012
   2     -451.0524838 0.80510        -450.2473800 0.92592        -451.1732957  16.330  15.176   2.218  98.298
   4     -451.1732957 0.82892        -450.3443771 0.91672        -451.2610977  10.771  10.332   2.838  76.811

 Number of TS in the path       =      6
 Number of cycles               =      4

 Elapsed time=                               539.77
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             33574 time=         249.61 %= 46.2
 OPTIM> # of energy+gradient+Hessian calls=       502 time=         142.64 %= 26.4
