
 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 11:56:40
  [-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.
 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=    -531.1555345     RMS force=    0.9704273099E-06
 OPTIM> Final energy  =    -532.5433804     RMS force=    0.8433586360E-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=     12652.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.30     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 210 RMS= 0.4161 Dev= 0.49% S= 26.36 time= 2.59
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   6.47

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     602 steps. Energy=    -533.5212667       time=       1.48
 Minus side of path:                     782 steps. Energy=    -532.7517099       time=       2.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5212667  5.4736         -528.0476746  4.7040         -532.7517099  15.992  11.800   3.584  29.851
        *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      1 steps with      1 missing connections, weight=     25305.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.30     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 805 RMS= 0.6125 Dev= 6.98% S= 29.13 time= 37.36
 Following    2 images are candidates for TS:   10   15  
 Converged to TS (number of iterations):        108
 Converged to TS (number of iterations):         42
 DNEB run yielded 2 true transition state(s) time=  15.27
 isnewts> transition state is the same as number        1 energy=     -528.0476746098
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     750 steps. Energy=    -532.7517099       time=       1.92
 Minus side of path:                    1061 steps. Energy=    -534.1460020       time=       2.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7517099  2.8257         -529.9259717  4.2200         -534.1460020  38.770  32.111   1.716  62.338
        Known (#4)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     590 steps. Energy=    -533.5212667       time=       1.47
 Minus side of path:                     783 steps. Energy=    -532.7517099       time=       2.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5212667  5.4736         -528.0476746  4.7040         -532.7517099  15.991  11.802   3.599  29.729
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     31534.    
 decide> The unconnected minima in the chain and their distances are:
     2       12.45     3     3       30.93     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_U using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2339 Dev= 0.04% S= 12.64 time= 0.66
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.61

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     629 steps. Energy=    -533.2558944       time=       1.56
 Minus side of path:                     703 steps. Energy=    -533.5212667       time=       1.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.2558944 0.20100         -533.0548898 0.46638         -533.5212667   8.143   6.438   6.366  16.809
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 3_U using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.8305116855    
 Double-ended search iterations= 315 RMS= 0.1106 Dev= 2.10% S= 37.47 time= 5.75
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.00

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     831 steps. Energy=    -532.7517099       time=       2.17
 Minus side of path:                     663 steps. Energy=    -531.1555345       time=       1.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.7517099  5.8581         -526.8936565  4.2619         -531.1555345  41.021  35.376   4.163  25.703
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1157.9    
 decide> The unconnected minima in the chain and their distances are:
     2       10.50     6 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 6_S using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.5423 Dev= 0.43% S= 10.63 time= 0.66
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=   3.97

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     884 steps. Energy=    -536.0490186       time=       2.35
 Minus side of path:                     623 steps. Energy=    -532.5433804       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0490186  3.5900         -532.4589750 0.84405E-01     -532.5433804  10.982  10.399   4.098  26.108
        *NEW* (Placed in 7)                                     Known (#2)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     301.69    
 decide> The unconnected minima in the chain and their distances are:
     7        6.71     6 
 

 tryconnect> 70-iteration DNEB run for minima 6_S and 7_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5569 Dev= 0.46% S= 6.85 time= 0.30
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.49

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     623 steps. Energy=    -536.0028407       time=       1.56
 Minus side of path:                     567 steps. Energy=    -533.2558944       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0028407  2.7518         -533.2510214 0.48730E-02     -533.2558944   4.670   4.474  11.131   9.613
        *NEW* (Placed in 8)                                     Known (#6)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     55.169    
 decide> The unconnected minima in the chain and their distances are:
     7        3.81     8 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 8_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0193 Dev= 0.01% S= 3.82 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.94

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     547 steps. Energy=    -536.0028407       time=       1.34
 Minus side of path:                     633 steps. Energy=    -536.0293735       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0028407 0.52611E-05     -536.0028354 0.26538E-01     -536.0293735   2.047   2.044  17.301   6.185
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     26.742    
 decide> The unconnected minima in the chain and their distances are:
     7        2.99     9 
 

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0074 Dev= 0.01% S= 2.99 time= 0.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   1.96

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     570 steps. Energy=    -536.0293735       time=       1.40
 Minus side of path:                     599 steps. Energy=    -536.0490186       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0293735 0.58145E-03     -536.0287920 0.20227E-01     -536.0490186   2.996   2.990   4.569  23.420
        Known (#9)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -531.1555345  4.2619        -526.8936565  5.8581        -532.7517099  41.021  35.376   4.163  25.703
   1     -532.7517099  4.7040        -528.0476746  5.4736        -533.5212667  15.992  11.800   3.584  29.851
   4     -533.5212667 0.46638        -533.0548898 0.20100        -533.2558944   8.143   6.438   6.366  16.809
   7     -533.2558944 0.48730E-02    -533.2510214  2.7518        -536.0028407   4.670   4.474  11.131   9.613
   8     -536.0028407 0.52610E-05    -536.0028354 0.26538E-01    -536.0293735   2.047   2.044  17.301   6.185
   9     -536.0293735 0.58145E-03    -536.0287920 0.20227E-01    -536.0490186   2.996   2.990   4.569  23.420
   6     -536.0490186  3.5900        -532.4589750 0.84405E-01    -532.5433804  10.982  10.399   4.098  26.108

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

 Elapsed time=                               132.89
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             42502 time=          84.66 %= 63.7
 OPTIM> # of energy+gradient+Hessian calls=       501 time=          26.90 %= 20.2
