
 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 21:45:53
  [-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=    -452.8246175     RMS force=    0.9928870956E-06
 OPTIM> Final energy  =    -447.5232955     RMS force=    0.9781509881E-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=    0.10668E+07
 decide> The unconnected minima in the chain and their distances are:
     2      102.18     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4901922056E-01
 Double-ended search iterations= 805 RMS= 0.0290 Dev= 5.58% S= 122.21 time= 139.83
 Following    2 images are candidates for TS:    9   18  
 Converged to TS (number of iterations):        173
 Converged to TS (number of iterations):        127
 DNEB run yielded 2 true transition state(s) time= 174.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1390 steps. Energy=    -446.7415011       time=      16.93
 Minus side of path:                    1741 steps. Energy=    -448.2880263       time=      24.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.7415011 0.30992         -446.4315849  1.8564         -448.2880263  58.105  49.505   1.797 121.312
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1343 steps. Energy=    -446.8513105       time=      15.98
 Minus side of path:                    1642 steps. Energy=    -447.5232955       time=      23.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8513105 0.13829E-02     -446.8499276 0.67337         -447.5232955  35.193  34.158   2.180 100.022
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=    0.10005E+06
 decide> The unconnected minima in the chain and their distances are:
     5       33.54     3     4       39.65     1 
 

 tryconnect> 350-iteration DNEB run for minima 3_U and 5_F using 10 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0327 Dev= 1.26% S= 36.33 time= 26.84
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         71
 DNEB run yielded 1 true transition state(s) time=  53.06

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1893 steps. Energy=    -448.2880263       time=      30.65
 Minus side of path:                    1420 steps. Energy=    -448.1414997       time=      19.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2880263  2.5495         -445.7385194  2.4030         -448.1414997  54.940  40.952   2.274  95.879
        Known (#4)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 4_U using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0325 Dev= 0.89% S= 41.48 time= 32.01
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=  36.68

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1280 steps. Energy=    -448.2880263       time=      14.88
 Minus side of path:                    1297 steps. Energy=    -448.7670328       time=      15.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2880263 0.26097E-02     -448.2854165 0.48162         -448.7670328  18.777  18.379   1.978 110.238
        Known (#4)                                              *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=     60902.    
 decide> The unconnected minima in the chain and their distances are:
     5       32.55     6     7       29.79     1 
 

 tryconnect> 315-iteration DNEB run for minima 5_F and 6_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0137 Dev= 0.46% S= 33.08 time= 21.60
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=  44.93

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1754 steps. Energy=    -447.5232955       time=      27.17
 Minus side of path:                    1471 steps. Energy=    -447.7433070       time=      20.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5232955 0.67404         -446.8492571 0.89405         -447.7433070  55.337  45.182   1.482 147.051
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 7_U using 8 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.1212 Dev= 0.68% S= 30.94 time= 17.28
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  40.30

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1256 steps. Energy=    -448.7670328       time=      14.75
 Minus side of path:                    1508 steps. Energy=    -452.8246175       time=      18.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7670328 0.60263E-01     -448.7067700  4.1178         -452.8246175  32.182  29.819   2.712  80.383
        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      5 steps with      1 missing connections, weight=     14.449    
 decide> The unconnected minima in the chain and their distances are:
     8        2.44     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_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= 0.4098 Dev= 2.79% S= 2.65 time= 1.10
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  23.82

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1284 steps. Energy=    -447.7433069       time=      15.81
 Minus side of path:                    1313 steps. Energy=    -448.1414997       time=      16.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.7433069 0.54965         -447.1936556 0.94784         -448.1414997   2.681   2.436  29.105   7.490
        Known (#8)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -452.8246175  4.1178        -448.7067700 0.60263E-01    -448.7670328  32.182  29.819   2.712  80.383
   4     -448.7670328 0.48162        -448.2854165 0.26097E-02    -448.2880263  18.777  18.379   1.978 110.238
   3     -448.2880263  2.5495        -445.7385194  2.4030        -448.1414997  54.940  40.952   2.274  95.879
   7     -448.1414997 0.94784        -447.1936556 0.54965        -447.7433070   2.681   2.436  29.105   7.490
   5     -447.7433070 0.89405        -446.8492571 0.67404        -447.5232955  55.337  45.182   1.482 147.051

 Number of TS in the path       =      5
 Number of cycles               =      4

 Elapsed time=                               886.22
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             62414 time=         468.82 %= 52.9
 OPTIM> # of energy+gradient+Hessian calls=       557 time=         165.36 %= 18.7
