
 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 09:33:22
  [-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=    -532.7952269     RMS force=    0.9497521978E-06
 OPTIM> Final energy  =    -531.5747104     RMS force=    0.8907024500E-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=     46794.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.04     1 
 

 tryconnect> 350-iteration DNEB run for minima 1_S and 2_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8720372697    
 Double-ended search iterations= 350 RMS= 0.5610 Dev= 1.39% S= 44.39 time= 7.03
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):        112
 Converged to TS (number of iterations):         55
 DNEB run yielded 2 true transition state(s) time=  17.35

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     585 steps. Energy=    -535.1145759       time=       1.43
 Minus side of path:                     613 steps. Energy=    -534.4788870       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1145759 0.97309         -534.1414823 0.33740         -534.4788870   7.449   6.251   9.428  11.349
        *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:                     691 steps. Energy=    -531.5747104       time=       1.73
 Minus side of path:                     701 steps. Energy=    -533.4267842       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.5747104  1.7964         -529.7783166  3.6485         -533.4267842  14.513   5.130  26.442   4.047
        Known (#2)                                              *NEW* (Placed in 5)
 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=     22178.    
 decide> The unconnected minima in the chain and their distances are:
     5       26.45     4     3       15.43     1 
 

 tryconnect> 245-iteration DNEB run for minima 4_U and 5_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.2392 Dev= 0.30% S= 29.25 time= 3.44
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   6.92

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     641 steps. Energy=    -533.5566983       time=       1.58
 Minus side of path:                     916 steps. Energy=    -535.1145759       time=       2.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5566983 0.69961         -532.8570868  2.2575         -535.1145759  21.220  18.040   2.231  47.961
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.6752 Dev= 0.54% S= 16.36 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.58

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     544 steps. Energy=    -535.1145759       time=       1.31
 Minus side of path:                     543 steps. Energy=    -535.1720621       time=       1.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1145759 0.25710         -534.8574758 0.31459         -535.1720621   4.713   4.591   4.488  23.843
        Known (#3)                                              *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=     12915.    
 decide> The unconnected minima in the chain and their distances are:
     5       20.97     6     7       15.46     1 
 

 tryconnect> 210-iteration DNEB run for minima 5_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.5985 Dev= 0.06% S= 22.11 time= 2.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   4.84
 isnewts> transition state is the same as number        3 energy=     -532.8570868051
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     653 steps. Energy=    -533.5566983       time=       1.62
 Minus side of path:                     922 steps. Energy=    -535.1145759       time=       2.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5566983 0.69961         -532.8570868  2.2575         -535.1145759  21.213  18.033   2.230  47.989
        Known (#6)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 1.1499 Dev= 0.54% S= 16.36 time= 1.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=   7.62
 isnewts> transition state is the same as number        4 energy=     -534.8574757733
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     554 steps. Energy=    -535.1145759       time=       1.34
 Minus side of path:                     550 steps. Energy=    -535.1720621       time=       1.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1145759 0.25710         -534.8574758 0.31459         -535.1720621   4.713   4.591   4.487  23.848
        Known (#3)                                              Known (#7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     15319.    
 decide> The unconnected minima in the chain and their distances are:
     2       21.16     6     4       18.01     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0958 Dev= 0.58% S= 22.99 time= 2.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        109
 DNEB run yielded 1 true transition state(s) time=  11.32

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     958 steps. Energy=    -534.6053308       time=       2.63
 Minus side of path:                     692 steps. Energy=    -533.4267842       time=       1.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6053308  1.6748         -532.9305500 0.49623         -533.4267842  31.993  27.524   2.611  40.986
        *NEW* (Placed in 8)                                     Known (#5)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1672 Dev= 0.50% S= 19.66 time= 1.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.90
 isnewts> transition state is the same as number        4 energy=     -534.8574757733
 tryconnect> Will not repeat search for TS      1 same as TS      4
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4094.1    
 decide> The unconnected minima in the chain and their distances are:
     8       16.00     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 8_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 140 RMS= 0.4570 Dev= 0.63% S= 17.44 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.13

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     619 steps. Energy=    -535.1720621       time=       1.52
 Minus side of path:                     579 steps. Energy=    -532.7503737       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1720621  2.9852         -532.1868376 0.56354         -532.7503737  14.979  12.342   3.249  32.935
        Known (#7)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     139.22    
 decide> The unconnected minima in the chain and their distances are:
     8        4.06     4     9        4.17     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_U and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1226 Dev= 0.15% S= 4.18 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.26
 isnewts> transition state is the same as number        1 energy=     -534.1414823429
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 9 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     609 steps. Energy=    -534.4788870       time=       1.49
 Minus side of path:                     582 steps. Energy=    -535.1145759       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.4788870 0.33740         -534.1414823 0.97309         -535.1145759   7.449   6.251   9.430  11.347
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0665 Dev= 0.10% S= 4.20 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.66

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     579 steps. Energy=    -532.7952269       time=       1.41
 Minus side of path:                     582 steps. Energy=    -532.7503737       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7952269 0.13267         -532.6625583 0.87815E-01     -532.7503737   4.396   4.167   5.879  18.200
        Known (#1)                                              Known (#9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 10 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     103.21    
 decide> The unconnected minima in the chain and their distances are:
     8        4.69     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 8_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4498 Dev= 0.05% S= 4.94 time= 0.28
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.40

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     571 steps. Energy=    -535.1145759       time=       1.39
 Minus side of path:                     562 steps. Energy=    -534.6053308       time=       1.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.1145759 0.54299         -534.5715879 0.33743E-01     -534.6053308   4.952   4.691  19.367   5.525
        Known (#3)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -532.7952269 0.13267        -532.6625583 0.87815E-01    -532.7503737   4.396   4.167   5.879  18.200
   8     -532.7503737 0.56354        -532.1868376  2.9852        -535.1720621  14.979  12.342   3.249  32.935
   4     -535.1720621 0.31459        -534.8574758 0.25710        -535.1145759   4.713   4.591   4.488  23.843
  11     -535.1145759 0.54299        -534.5715879 0.33743E-01    -534.6053308   4.952   4.691  19.367   5.525
   7     -534.6053308  1.6748        -532.9305500 0.49623        -533.4267842  31.993  27.524   2.611  40.986
   2     -533.4267842  3.6485        -529.7783166  1.7964        -531.5747104  14.513   5.130  26.442   4.047

 Number of TS in the path       =      6
 Number of cycles               =      7

 Elapsed time=                               134.91
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             34479 time=          68.71 %= 50.9
 OPTIM> # of energy+gradient+Hessian calls=       709 time=          38.39 %= 28.5
