
 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 11:42:19
  [-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=    -449.2428646     RMS force=    0.9767780989E-06
 OPTIM> Final energy  =    -451.4137263     RMS force=    0.9936229168E-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=    0.18936E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.42     1 
 

 tryconnect> 595-iteration DNEB run for minima 1_S and 2_F using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1433940004    
 Double-ended search iterations= 595 RMS= 0.0315 Dev= 5.53% S= 68.57 time= 76.58
 Following    2 images are candidates for TS:    7    9  
 Failed to converge to TS (number of iterations):        251
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 255.65
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.37872E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.42     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1580918855    
 Double-ended search iterations= 805 RMS= 0.0234 Dev= 5.09% S= 69.45 time= 137.69
 Following    2 images are candidates for TS:    9   12  
 Failed to converge to TS (number of iterations):        251
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 239.13
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> There appear to be no connections left to try in DIJKSTRA
 decide> Increasing maximum number of images to     25 and clearing weights
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     4000.0    
 decide> The unconnected minima in the chain and their distances are:
     2       10.00     1 
 

 tryconnect> 875-iteration DNEB run for minima 1_S and 2_F using 25 images  (DNEB attempt #4)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 875 RMS= 0.0369 Dev= 7.64% S= 68.96 time= 162.42
 Following    2 images are candidates for TS:   10   13  
 Converged to TS (number of iterations):         38
 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= 162.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1688 steps. Energy=    -449.2428646       time=      22.39
 Minus side of path:                    1330 steps. Energy=    -449.7929330       time=      15.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2428646  1.9574         -447.2854930  2.5074         -449.7929330  50.016  44.349   3.172  68.720
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     97770.    
 decide> The unconnected minima in the chain and their distances are:
     2       46.07     3 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 3_S using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0378 Dev= 4.58% S= 51.13 time= 44.80
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  60.66

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1373 steps. Energy=    -449.7929330       time=      15.54
 Minus side of path:                    1385 steps. Energy=    -449.9537038       time=      15.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7929330 0.38713         -449.4058017 0.54790         -449.9537038  44.094  36.781   1.719 126.825
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     6733.3    
 decide> The unconnected minima in the chain and their distances are:
     2       18.88     4 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 4_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1616 Dev= 1.74% S= 21.31 time= 6.61
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        130
 DNEB run yielded 1 true transition state(s) time=  66.16

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1267 steps. Energy=    -449.9537038       time=      13.38
 Minus side of path:                    1334 steps. Energy=    -450.7647331       time=      14.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9537038 0.90046E-01     -449.8636582 0.90107         -450.7647331   9.828   8.702   1.719 126.829
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     5422.3    
 decide> The unconnected minima in the chain and their distances are:
     2       17.57     5 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 5_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 175 RMS= 0.2263 Dev= 2.03% S= 20.15 time= 6.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=  61.38

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1378 steps. Energy=    -451.6433888       time=      14.77
 Minus side of path:                    2615 steps. Energy=    -455.4122156       time=      43.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6433888 0.88168         -450.7617071  4.6505         -455.4122156  74.777  68.331   1.621 134.496
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     10845.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.57     5 
 

 tryconnect> 875-iteration DNEB run for minima 2_F and 5_S using 25 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 875 RMS= 0.0509 Dev= 4.31% S= 25.45 time= 166.02
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=  40.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1642 steps. Energy=    -451.4137263       time=      21.42
 Minus side of path:                    1332 steps. Energy=    -449.7929330       time=      15.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4137263  6.9470         -444.4667172  5.3262         -449.7929330  47.755  46.113   1.727 126.194
        Known (#2)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -449.2428646  1.9574        -447.2854930  2.5074        -449.7929330  50.016  44.349   3.172  68.720
   5     -449.7929330  5.3262        -444.4667172  6.9470        -451.4137263  47.755  46.113   1.727 126.194

 Number of TS in the path       =      2
 Number of cycles               =      7

 Elapsed time=                              1678.67
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            111467 time=         829.44 %= 49.4
 OPTIM> # of energy+gradient+Hessian calls=      1662 time=         472.40 %= 28.1
