
 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 05/23/2012 at 21:10:05
  [-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=    -451.1590092     RMS force=    0.8916794710E-06
 OPTIM> Final energy  =    -444.2194267     RMS force=    0.8015893517E-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=    0.30468E+06
 decide> The unconnected minima in the chain and their distances are:
     2       67.29     1 
 

 tryconnect> 700-iteration DNEB run for minima 1_S and 2_F using 20 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4855829818    
 Double-ended search iterations= 700 RMS= 0.0496 Dev= 4.79% S= 77.49 time= 107.27
 Following    2 images are candidates for TS:   12   19  
 Converged to TS (number of iterations):        104
 Converged to TS (number of iterations):         49
 DNEB run yielded 2 true transition state(s) time= 124.79

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1275 steps. Energy=    -451.1590092       time=      14.61
 Minus side of path:                    1306 steps. Energy=    -450.7047863       time=      15.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.1590092 0.87907         -450.2799427 0.42484         -450.7047863   9.731   8.928  19.997  10.902
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1313 steps. Energy=    -444.2158652       time=      17.81
 Minus side of path:                    1477 steps. Energy=    -448.0685279       time=      21.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.2158652 0.80102E-01     -444.1357635  3.9328         -448.0685279  37.930  35.056   3.653  59.676
        *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=    0.13241E+06
 decide> The unconnected minima in the chain and their distances are:
     2        6.12     4     5       50.94     3 
 

 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= 0.0175 Dev= 0.00% S= 6.12 time= 1.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  22.29

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1263 steps. Energy=    -444.2194267       time=      16.30
 Minus side of path:                    1288 steps. Energy=    -444.2158651       time=      16.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.2194267 0.66847E-02     -444.2127421 0.31231E-02     -444.2158651   6.125   6.119   2.769  78.730
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 525-iteration DNEB run for minima 3_S and 5_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0464 Dev= 3.79% S= 56.74 time= 59.85
 Following    2 images are candidates for TS:   10   14  
 Converged to TS (number of iterations):         86
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 183.43

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1417 steps. Energy=    -448.8985101       time=      16.61
 Minus side of path:                    2181 steps. Energy=    -450.5085471       time=      33.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8985101  1.5026         -447.3959288  3.1126         -450.5085471  88.743  77.422   1.443 151.107
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     40700.    
 decide> The unconnected minima in the chain and their distances are:
     5        2.95     6     7       34.39     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1165 Dev= 0.42% S= 3.04 time= 1.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  21.55

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1272 steps. Energy=    -448.0685279       time=      14.09
 Minus side of path:                    1281 steps. Energy=    -448.8985101       time=      14.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.0685279 0.15350         -447.9150300 0.98348         -448.8985101   3.014   2.951   8.457  25.778
        Known (#5)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 7_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0257 Dev= 0.55% S= 35.59 time= 26.40
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  27.58

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1286 steps. Energy=    -450.8535168       time=      13.97
 Minus side of path:                    1281 steps. Energy=    -450.5085471       time=      14.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.8535168 0.82259         -450.0309259 0.47762         -450.5085471   9.303   8.585  20.402  10.685
        *NEW* (Placed in 8)                                     Known (#7)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     42073.    
 decide> The unconnected minima in the chain and their distances are:
     8       34.78     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 8_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0361 Dev= 0.23% S= 35.39 time= 26.30
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  29.08

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1277 steps. Energy=    -451.1590092       time=      13.87
 Minus side of path:                    1509 steps. Energy=    -450.8535168       time=      17.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.1590092 0.80436         -450.3546485 0.49887         -450.8535168  39.339  34.906   1.530 142.479
        Known (#1)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   7     -451.1590092 0.80436        -450.3546485 0.49887        -450.8535168  39.339  34.906   1.530 142.479
   6     -450.8535168 0.82259        -450.0309259 0.47762        -450.5085471   9.303   8.585  20.402  10.685
   4     -450.5085471  3.1126        -447.3959288  1.5026        -448.8985101  88.743  77.422   1.443 151.107
   5     -448.8985101 0.98348        -447.9150300 0.15350        -448.0685279   3.014   2.951   8.457  25.778
   2     -448.0685279  3.9328        -444.1357635 0.80102E-01    -444.2158652  37.930  35.056   3.653  59.676
   3     -444.2158652 0.31231E-02    -444.2127421 0.66847E-02    -444.2194267   6.125   6.119   2.769  78.730

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

 Elapsed time=                               871.51
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             60583 time=         458.20 %= 52.6
 OPTIM> # of energy+gradient+Hessian calls=       588 time=         174.73 %= 20.0
