
 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 12:09:51
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -452.5640902     RMS force=    0.7711690069E-06
 OPTIM> Final energy  =    -454.9873715     RMS force=    0.9333630019E-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=    0.49512E+06
 decide> The unconnected minima in the chain and their distances are:
     2       79.11     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6569044378E-01
 Double-ended search iterations= 805 RMS= 0.1228 Dev= 4.06% S= 100.93 time= 140.76
 Following    2 images are candidates for TS:    6   13  
 Converged to TS (number of iterations):        101
 Converged to TS (number of iterations):         48
 DNEB run yielded 2 true transition state(s) time=  96.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1306 steps. Energy=    -453.8354284       time=      13.85
 Minus side of path:                    1300 steps. Energy=    -452.5640902       time=      13.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8354284  1.3686         -452.4668486 0.97242E-01     -452.5640902  17.399  17.181   1.448 150.582
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1281 steps. Energy=    -455.6165745       time=      13.96
 Minus side of path:                    1275 steps. Energy=    -453.6576303       time=      13.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.6165745  2.6497         -452.9668332 0.69080         -453.6576303  19.344  18.518   6.353  34.312
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.23625E+06
 decide> The unconnected minima in the chain and their distances are:
     2       61.15     4     5       19.61     3 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 4_U using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3840784197E-01
 Double-ended search iterations= 630 RMS= 0.0277 Dev= 1.15% S= 72.44 time= 84.76
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  34.33

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1472 steps. Energy=    -456.9279803       time=      16.06
 Minus side of path:                    1612 steps. Energy=    -454.9873715       time=      18.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.9279803  3.4661         -453.4618382  1.5255         -454.9873715  67.528  52.342   3.033  71.880
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_S and 5_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0799 Dev= 0.26% S= 20.20 time= 6.61
 Following    2 images are candidates for TS:    2    5  
 Converged to TS (number of iterations):        152
 Converged to TS (number of iterations):         35
 DNEB run yielded 2 true transition state(s) time= 131.80

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1248 steps. Energy=    -455.7190744       time=      12.75
 Minus side of path:                    1316 steps. Energy=    -457.1140484       time=      13.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.7190744 0.29231E-01     -455.6898438  1.4242         -457.1140484  32.946  32.596   2.575  84.662
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1293 steps. Energy=    -457.1140484       time=      13.42
 Minus side of path:                    1315 steps. Energy=    -454.0537354       time=      13.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.1140484  4.1461         -452.9679755  1.0858         -454.0537354  21.277  15.727   2.305  94.582
        Known (#8)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     45555.    
 decide> The unconnected minima in the chain and their distances are:
     6       34.70     4     5       13.23     8     8       11.38     3 
 

 tryconnect> 350-iteration DNEB run for minima 4_U and 6_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0211 Dev= 0.26% S= 35.27 time= 26.22
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  25.08

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1383 steps. Energy=    -456.9279803       time=      14.69
 Minus side of path:                    1277 steps. Energy=    -455.6165745       time=      13.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.9279803  1.3489         -455.5790532 0.37521E-01     -455.6165745  34.868  34.698   1.821 119.725
        Known (#6)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 5_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1222 Dev= 0.21% S= 13.47 time= 2.39
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  28.82
 isnewts> transition state is the same as number        5 energy=     -452.9679755470
 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:                    1273 steps. Energy=    -457.1140484       time=      13.12
 Minus side of path:                    1326 steps. Energy=    -454.0537354       time=      13.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.1140484  4.1461         -452.9679755  1.0858         -454.0537354  21.277  15.727   2.304  94.601
        Known (#8)                                              Known (#9)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 3_S and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0574 Dev= 0.03% S= 11.40 time= 2.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=  31.33

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1299 steps. Energy=    -456.5998337       time=      13.52
 Minus side of path:                    1254 steps. Energy=    -453.8354284       time=      12.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.5998337  2.8531         -453.7467067 0.88722E-01     -453.8354284  14.182  13.169   5.710  38.178
        *NEW* (Placed in 10)                                    Known (#3)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     4285.4    
 decide> The unconnected minima in the chain and their distances are:
     5       14.47     9     8       10.79    10 
 

 tryconnect> 140-iteration DNEB run for minima 5_F and 9_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0712 Dev= 0.03% S= 14.57 time= 4.24
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=  32.28

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1293 steps. Energy=    -454.0537354       time=      13.43
 Minus side of path:                    1282 steps. Energy=    -453.6576303       time=      13.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.0537354 0.50193         -453.5518034 0.10583         -453.6576303  14.841  14.471   2.487  87.656
        Known (#9)                                              Known (#5)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 8_F and 10_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1598 Dev= 0.24% S= 10.86 time= 2.39
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  21.13

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1279 steps. Energy=    -456.5998337       time=      13.23
 Minus side of path:                    1275 steps. Energy=    -457.1140484       time=      13.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.5998337  1.0059         -455.5939643  1.5201         -457.1140484  12.078  10.787   2.241  97.288
        Known (#10)                                             Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -452.5640902 0.97242E-01    -452.4668486  1.3686        -453.8354284  17.399  17.181   1.448 150.582
   8     -453.8354284 0.88722E-01    -453.7467067  2.8531        -456.5998337  14.182  13.169   5.710  38.178
  10     -456.5998337  1.0059        -455.5939643  1.5201        -457.1140484  12.078  10.787   2.241  97.288
   5     -457.1140484  4.1461        -452.9679755  1.0858        -454.0537354  21.277  15.727   2.305  94.582
   9     -454.0537354 0.50193        -453.5518034 0.10583        -453.6576303  14.841  14.471   2.487  87.656
   2     -453.6576303 0.69080        -452.9668332  2.6497        -455.6165745  19.344  18.518   6.353  34.312
   6     -455.6165745 0.37521E-01    -455.5790532  1.3489        -456.9279803  34.868  34.698   1.821 119.725
   3     -456.9279803  3.4661        -453.4618382  1.5255        -454.9873715  67.528  52.342   3.033  71.880

 Number of TS in the path       =      8
 Number of cycles               =      4

 Elapsed time=                               948.95
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             77260 time=         577.37 %= 60.8
 OPTIM> # of energy+gradient+Hessian calls=       563 time=         155.04 %= 16.3
