
 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 10:05:37
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    17
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>  321 Cartesian coordinates will be optimised for  107 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 =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -528.7521847     RMS force=    0.9716972398E-06
 OPTIM> Final energy  =    -529.8876944     RMS force=    0.9405041789E-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=     29875.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.03     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.1196 Dev= 1.34% S= 46.52 time= 5.81
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         44
 Converged to TS (number of iterations):         25
 DNEB run yielded 2 true transition state(s) time=   8.06

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     649 steps. Energy=    -528.7521847       time=       1.61
 Minus side of path:                     637 steps. Energy=    -529.1188110       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.7521847  3.2970         -525.4551870  3.6636         -529.1188110  29.562  26.317   3.675  29.113
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     704 steps. Energy=    -529.3393685       time=       1.84
 Minus side of path:                     702 steps. Energy=    -529.3617448       time=       1.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.3393685  4.3883         -524.9510905  4.4107         -529.3617448  20.249  10.169  15.382   6.956
        *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=     556.54    
 decide> The unconnected minima in the chain and their distances are:
     2        5.83     5     4        7.10     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1074 Dev= 0.04% S= 5.85 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   6.67

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     547 steps. Energy=    -530.0473052       time=       1.33
 Minus side of path:                     572 steps. Energy=    -530.2082852       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.0473052 0.15464E-01     -530.0318416 0.17644         -530.2082852   4.745   4.541  18.048   5.929
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0572 Dev= 0.03% S= 7.13 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   2.90

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     600 steps. Energy=    -529.1188110       time=       1.47
 Minus side of path:                     660 steps. Energy=    -529.3393685       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.1188110 0.36112E-01     -529.0826988 0.25667         -529.3393685   7.277   7.106   5.463  19.585
        Known (#3)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     396.20    
 decide> The unconnected minima in the chain and their distances are:
     2        5.83     5 
 

 tryconnect> 455-iteration DNEB run for minima 2_F and 5_S using 13 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0087 Dev= 2.23% S= 7.02 time= 12.06
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=   3.70

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     526 steps. Energy=    -529.8147271       time=       1.30
 Minus side of path:                     584 steps. Energy=    -530.0473052       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8147271 0.10597E-02     -529.8136674 0.23364         -530.0473052   1.068   1.056   8.923  11.992
        *NEW* (Placed in 8)                                     Known (#6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     594.29    
 decide> The unconnected minima in the chain and their distances are:
     2        5.83     5 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 5_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 805 RMS= 0.0216 Dev= 14.11% S= 7.56 time= 37.51
 Following    1 images are candidates for TS:   20  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.92

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     666 steps. Energy=    -529.8876944       time=       1.66
 Minus side of path:                     551 steps. Energy=    -529.8147271       time=       1.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8876944 0.76188E-01     -529.8115067 0.32203E-02     -529.8147271   4.734   4.629   5.149  20.781
        Known (#2)                                              Known (#8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     562.04    
 decide> The unconnected minima in the chain and their distances are:
     8        8.25     5 
 

 tryconnect> 70-iteration DNEB run for minima 5_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3423 Dev= 0.03% S= 8.30 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         92
 DNEB run yielded 1 true transition state(s) time=   8.79

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     571 steps. Energy=    -529.3617448       time=       1.39
 Minus side of path:                     701 steps. Energy=    -530.0473052       time=       1.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.3617448 0.10047E-01     -529.3516973 0.69561         -530.0473052   8.785   8.528   5.237  20.433
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -528.7521847  3.2970        -525.4551870  3.6636        -529.1188110  29.562  26.317   3.675  29.113
   4     -529.1188110 0.36112E-01    -529.0826988 0.25667        -529.3393685   7.277   7.106   5.463  19.585
   2     -529.3393685  4.3883        -524.9510905  4.4107        -529.3617448  20.249  10.169  15.382   6.956
   7     -529.3617448 0.10047E-01    -529.3516973 0.69561        -530.0473052   8.785   8.528   5.237  20.433
   5     -530.0473052 0.23364        -529.8136674 0.10597E-02    -529.8147271   1.068   1.056   8.923  11.992
   6     -529.8147271 0.32203E-02    -529.8115067 0.76188E-01    -529.8876944   4.734   4.629   5.149  20.781

 Number of TS in the path       =      6
 Number of cycles               =      5

 Elapsed time=                               113.62
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             41452 time=          82.55 %= 72.7
 OPTIM> # of energy+gradient+Hessian calls=       304 time=          16.31 %= 14.4
