
 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 10:48:06
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -530.7044326     RMS force=    0.8671140489E-06
 OPTIM> Final energy  =    -530.1269937     RMS force=    0.9812265228E-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=     2229.2    
 decide> The unconnected minima in the chain and their distances are:
     2       13.06     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5571 Dev= 0.78% S= 14.65 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   4.90

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     600 steps. Energy=    -529.5142732       time=       1.50
 Minus side of path:                     723 steps. Energy=    -531.0874248       time=       1.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.5142732  2.1775         -527.3367637  3.7507         -531.0874248   9.139   7.641  12.302   8.698
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1998.9    
 decide> The unconnected minima in the chain and their distances are:
     2       10.81     4     3        9.03     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1221 Dev= 0.09% S= 11.10 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.16

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     577 steps. Energy=    -530.6559234       time=       1.42
 Minus side of path:                     577 steps. Energy=    -530.3227775       time=       1.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.6559234  1.0322         -529.6237512 0.69903         -530.3227775   7.889   7.548   1.789  59.807
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.6653 Dev= 0.41% S= 9.44 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   4.07

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     605 steps. Energy=    -531.0960020       time=       1.51
 Minus side of path:                     596 steps. Energy=    -529.5142732       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.0960020  1.6876         -529.4084284 0.10584         -529.5142732  10.470   9.576   7.039  15.202
        *NEW* (Placed in 7)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     347.81    
 decide> The unconnected minima in the chain and their distances are:
     2        4.34     6     5        5.33     4     7        4.85     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.1720 Dev= 0.10% S= 4.85 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.55

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     559 steps. Energy=    -530.1284781       time=       1.36
 Minus side of path:                     531 steps. Energy=    -530.1269937       time=       1.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1284781 0.18249E-02     -530.1266531 0.34058E-03     -530.1269937   0.378   0.378  11.595   9.229
        *NEW* (Placed in 8)                                     Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0925 Dev= 0.07% S= 5.50 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.10

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     571 steps. Energy=    -530.7556538       time=       1.40
 Minus side of path:                     552 steps. Energy=    -530.6559234       time=       1.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7556538 0.12157         -530.6340806 0.21843E-01     -530.6559234   3.501   3.486   2.901  36.879
        *NEW* (Placed in 9)                                     Known (#5)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3655 Dev= 0.24% S= 5.10 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.31

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     562 steps. Energy=    -530.7044326       time=       1.37
 Minus side of path:                     589 steps. Energy=    -531.0960020       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7044326 0.25148E-01     -530.6792850 0.41672         -531.0960020   5.446   4.855  21.078   5.076
        Known (#1)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     200.29    
 decide> The unconnected minima in the chain and their distances are:
     8        4.32     6     9        4.93     4 
 

 tryconnect> 70-iteration DNEB run for minima 6_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.2725 Dev= 0.12% S= 4.83 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.31
 isnewts> transition state is the same as number        4 energy=     -530.1266531349
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     577 steps. Energy=    -530.1284781       time=       1.42
 Minus side of path:                     541 steps. Energy=    -530.1269937       time=       1.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1284781 0.18249E-02     -530.1266531 0.34058E-03     -530.1269937   0.378   0.378  11.594   9.229
        Known (#8)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3338 Dev= 0.14% S= 5.28 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.12

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     533 steps. Energy=    -530.7556538       time=       1.29
 Minus side of path:                     747 steps. Energy=    -531.0874248       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7556538 0.12466E-01     -530.7431876 0.34424         -531.0874248   5.095   4.973  17.990   5.948
        Known (#9)                                              Known (#4)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     161.24    
 decide> The unconnected minima in the chain and their distances are:
     8        4.32     6 
 

 tryconnect> 315-iteration DNEB run for minima 6_S and 8_F using 9 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0045 Dev= 0.19% S= 5.09 time= 5.73
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.46

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     584 steps. Energy=    -530.1284781       time=       1.47
 Minus side of path:                     614 steps. Energy=    -530.3227775       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1284781 0.14347E-01     -530.1141316 0.20865         -530.3227775   4.919   4.324  31.582   3.388
        Known (#8)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -530.7044326 0.25148E-01    -530.6792850 0.41672        -531.0960020   5.446   4.855  21.078   5.076
   3     -531.0960020  1.6876        -529.4084284 0.10584        -529.5142732  10.470   9.576   7.039  15.202
   1     -529.5142732  2.1775        -527.3367637  3.7507        -531.0874248   9.139   7.641  12.302   8.698
   8     -531.0874248 0.34424        -530.7431876 0.12466E-01    -530.7556538   5.095   4.973  17.990   5.948
   5     -530.7556538 0.12157        -530.6340806 0.21843E-01    -530.6559234   3.501   3.486   2.901  36.879
   2     -530.6559234  1.0322        -529.6237512 0.69903        -530.3227775   7.889   7.548   1.789  59.807
   9     -530.3227775 0.20865        -530.1141316 0.14347E-01    -530.1284781   4.919   4.324  31.582   3.388
   4     -530.1284781 0.18249E-02    -530.1266531 0.34058E-03    -530.1269937   0.378   0.378  11.595   9.229

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                                68.85
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             20619 time=          41.45 %= 60.2
 OPTIM> # of energy+gradient+Hessian calls=       255 time=          13.94 %= 20.2
