
 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 09:59:52
  [-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=    -534.6711754     RMS force=    0.9676615577E-06
 OPTIM> Final energy  =    -528.7249325     RMS force=    0.7703196372E-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=     27779.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.29     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= 0.2618 Dev= 1.52% S= 39.16 time= 5.82
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):        103
 Converged to TS (number of iterations):         38
 DNEB run yielded 2 true transition state(s) time=  14.56

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     567 steps. Energy=    -533.5038575       time=       1.38
 Minus side of path:                     698 steps. Energy=    -535.2417289       time=       1.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5038575 0.11652         -533.3873357  1.8544         -535.2417289  16.171  15.519   6.434  16.629
        *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:                    1095 steps. Energy=    -534.1997122       time=       3.14
 Minus side of path:                     616 steps. Energy=    -528.7249325       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122  7.0282         -527.1714739  1.5535         -528.7249325  27.157  25.232   2.968  36.049
        *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=     2323.8    
 decide> The unconnected minima in the chain and their distances are:
     5       13.25     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 3.1151 Dev= 0.48% S= 18.41 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   5.74

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     571 steps. Energy=    -534.6787748       time=       1.39
 Minus side of path:                     565 steps. Energy=    -535.0845517       time=       1.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6787748 0.95518E-01     -534.5832573 0.50129         -535.0845517   5.651   5.208  18.259   5.860
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     1675.7    
 decide> The unconnected minima in the chain and their distances are:
     5       11.38     6     6        5.80     4     4        1.69     1 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 6_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.8248 Dev= 0.23% S= 16.26 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=   5.98

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     670 steps. Energy=    -534.5278451       time=       1.67
 Minus side of path:                     709 steps. Energy=    -535.3372163       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5278451  3.4847         -531.0431372  4.2941         -535.3372163  17.765  10.831  12.538   8.534
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0730 Dev= 0.01% S= 5.81 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.26

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     575 steps. Energy=    -535.2417289       time=       1.40
 Minus side of path:                     535 steps. Energy=    -534.6787748       time=       1.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.2417289 0.61749         -534.6242380 0.54537E-01     -534.6787748   5.860   5.805   3.841  27.860
        Known (#4)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.2505 Dev= 2.00% S= 2.32 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.23

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     562 steps. Energy=    -534.6711754       time=       1.37
 Minus side of path:                     570 steps. Energy=    -535.2417289       time=       1.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.6711754  8.1711         -526.5000622  8.7417         -535.2417289   2.627   1.690  57.801   1.851
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     436.39    
 decide> The unconnected minima in the chain and their distances are:
     5        7.38     8     9        3.26     7 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1490 Dev= 0.04% S= 7.43 time= 0.40
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.42

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     541 steps. Energy=    -534.5864911       time=       1.31
 Minus side of path:                     578 steps. Energy=    -534.7851393       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5864911 0.79550E-01     -534.5069412 0.27820         -534.7851393   5.365   5.094   3.422  31.265
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0162 Dev= 0.01% S= 3.26 time= 0.35
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):          8
 DNEB run yielded 1 true transition state(s) time=   1.67

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     495 steps. Energy=    -535.0845517       time=       1.18
 Minus side of path:                     508 steps. Energy=    -535.3372163       time=       1.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -535.0845517 0.97871E-02     -535.0747646 0.26245         -535.3372163   3.275   3.262   4.173  25.639
        Known (#7)                                              Known (#9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      2 missing connections, weight=     167.61    
 decide> The unconnected minima in the chain and their distances are:
     5        5.12    10    11        3.23     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1578 Dev= 0.48% S= 5.51 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.52

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     570 steps. Energy=    -534.1997122       time=       1.39
 Minus side of path:                     577 steps. Energy=    -534.5864911       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122 0.78097E-01     -534.1216152 0.46488         -534.5864911   5.520   5.120  19.584   5.464
        Known (#5)                                              Known (#10)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 8_S and 11_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0837 Dev= 0.05% S= 3.27 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.29

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     558 steps. Energy=    -534.5278451       time=       1.37
 Minus side of path:                     574 steps. Energy=    -534.7851393       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5278451 0.65089E-01     -534.4627563 0.32238         -534.7851393   3.328   3.225   9.808  10.909
        Known (#8)                                              Known (#11)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -534.6711754  8.1711        -526.5000622  8.7417        -535.2417289   2.627   1.690  57.801   1.851
   5     -535.2417289 0.61749        -534.6242380 0.54537E-01    -534.6787748   5.860   5.805   3.841  27.860
   3     -534.6787748 0.95518E-01    -534.5832573 0.50129        -535.0845517   5.651   5.208  18.259   5.860
   8     -535.0845517 0.97871E-02    -535.0747646 0.26245        -535.3372163   3.275   3.262   4.173  25.639
   4     -535.3372163  4.2941        -531.0431372  3.4847        -534.5278451  17.765  10.831  12.538   8.534
  10     -534.5278451 0.65089E-01    -534.4627563 0.32238        -534.7851393   3.328   3.225   9.808  10.909
   7     -534.7851393 0.27820        -534.5069412 0.79550E-01    -534.5864911   5.365   5.094   3.422  31.265
   9     -534.5864911 0.46488        -534.1216152 0.78097E-01    -534.1997122   5.520   5.120  19.584   5.464
   2     -534.1997122  7.0282        -527.1714739  1.5535        -528.7249325  27.157  25.232   2.968  36.049

 Number of TS in the path       =      9
 Number of cycles               =      5

 Elapsed time=                                82.17
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             22827 time=          45.98 %= 56.0
 OPTIM> # of energy+gradient+Hessian calls=       356 time=          19.05 %= 23.2
