
 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 12:09:13
  [-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=    -448.4521141     RMS force=    0.9731429795E-06
 OPTIM> Final energy  =    -443.7475080     RMS force=    0.9145887768E-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=     26271.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.73     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 2_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 280 RMS= 0.5077 Dev= 0.87% S= 35.52 time= 16.36
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):        216
 Converged to TS (number of iterations):         34
 DNEB run yielded 2 true transition state(s) time= 155.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1215 steps. Energy=    -448.6799982       time=      14.58
 Minus side of path:                    1283 steps. Energy=    -448.5798885       time=      14.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6799982 0.34511         -448.3348910 0.24500         -448.5798885  16.936  15.631   2.425  89.909
        *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:                    1393 steps. Energy=    -447.5490106       time=      14.95
 Minus side of path:                    1291 steps. Energy=    -443.7475080       time=      13.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5490106  3.8454         -443.7035743 0.43934E-01     -443.7475080  21.665  18.029   5.185  42.048
        *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      2 steps with      1 missing connections, weight=     7044.9    
 decide> The unconnected minima in the chain and their distances are:
     5       19.17     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 5_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 175 RMS= 1.2729 Dev= 1.37% S= 25.20 time= 6.06
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 126.83
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     14090.    
 decide> The unconnected minima in the chain and their distances are:
     5       19.17     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.644356330    
 Double-ended search iterations= 805 RMS= 0.0785 Dev= 5.47% S= 33.20 time= 135.78
 Following    2 images are candidates for TS:    7   16  
 Converged to TS (number of iterations):         98
 Converged to TS (number of iterations):        219
 DNEB run yielded 2 true transition state(s) time= 181.15

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1625 steps. Energy=    -448.4521141       time=      23.00
 Minus side of path:                    1309 steps. Energy=    -447.8906320       time=      16.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4521141  1.2899         -447.1621974 0.72843         -447.8906320  42.320  30.337   2.133 102.193
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1790 steps. Energy=    -451.6180121       time=      27.62
 Minus side of path:                    1367 steps. Energy=    -448.8105079       time=      17.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6180121  3.6983         -447.9196827 0.89083         -448.8105079  44.756  33.513   3.966  54.971
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     52542.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.73     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 805 RMS= 0.0356 Dev= 5.63% S= 50.37 time= 137.06
 Following    2 images are candidates for TS:    8   13  
 Converged to TS (number of iterations):        128
 Converged to TS (number of iterations):        154
 DNEB run yielded 2 true transition state(s) time= 164.91
 isnewts> transition state is the same as number        1 energy=     -448.3348910009
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1348 steps. Energy=    -447.8906320       time=      17.67
 Minus side of path:                    1881 steps. Energy=    -448.1429450       time=      27.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8906320  1.0416         -446.8489860  1.2940         -448.1429450  50.179  49.033   1.760 123.871
        Known (#6)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1188 steps. Energy=    -448.6799982       time=      14.58
 Minus side of path:                    1258 steps. Energy=    -448.5798885       time=      14.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6799982 0.34511         -448.3348910 0.24500         -448.5798885  16.936  15.631   2.425  89.900
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     31650.    
 decide> The unconnected minima in the chain and their distances are:
     5       31.63     9 
 

 tryconnect> 315-iteration DNEB run for minima 5_F and 9_S using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0450 Dev= 0.49% S= 34.03 time= 21.23
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        139
 DNEB run yielded 1 true transition state(s) time=  71.14

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    2355 steps. Energy=    -451.6180121       time=      35.27
 Minus side of path:                    1283 steps. Energy=    -447.5490106       time=      13.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6180121  4.1412         -447.4767840 0.72227E-01     -447.5490106  57.396  55.935   3.102  70.276
        Known (#7)                                              Known (#5)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     16722.    
 decide> The unconnected minima in the chain and their distances are:
     8       25.57     9 
 

 tryconnect> 245-iteration DNEB run for minima 8_F and 9_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 1.4161 Dev= 0.32% S= 27.87 time= 12.83
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  36.49

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1432 steps. Energy=    -448.8105079       time=      16.66
 Minus side of path:                    1290 steps. Energy=    -448.1429450       time=      13.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8105079  1.9538         -446.8567482  1.2862         -448.1429450  30.402  25.595   3.186  68.422
        Known (#8)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -448.4521141  1.2899        -447.1621974 0.72843        -447.8906320  42.320  30.337   2.133 102.193
   5     -447.8906320  1.0416        -446.8489860  1.2940        -448.1429450  50.179  49.033   1.760 123.871
   8     -448.1429450  1.2862        -446.8567482  1.9538        -448.8105079  30.402  25.595   3.186  68.422
   4     -448.8105079 0.89083        -447.9196827  3.6983        -451.6180121  44.756  33.513   3.966  54.971
   7     -451.6180121  4.1412        -447.4767840 0.72227E-01    -447.5490106  57.396  55.935   3.102  70.276
   2     -447.5490106  3.8454        -443.7035743 0.43934E-01    -443.7475080  21.665  18.029   5.185  42.048

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

 Elapsed time=                              1362.18
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             83371 time=         620.61 %= 45.6
 OPTIM> # of energy+gradient+Hessian calls=      1288 time=         361.98 %= 26.6
