
 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 10:28:48
  [-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=    -530.5350581     RMS force=    0.9544216290E-06
 OPTIM> Final energy  =    -531.5574421     RMS force=    0.9663162160E-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=     3918.2    
 decide> The unconnected minima in the chain and their distances are:
     2       15.77     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 140 RMS= 1.9491 Dev= 1.43% S= 22.26 time= 1.14
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.82

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     590 steps. Energy=    -526.4092652       time=       1.51
 Minus side of path:                     605 steps. Energy=    -530.5350581       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -526.4092652  3.6203         -522.7889601  7.7461         -530.5350581   6.604   5.293  20.655   5.180
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     3368.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.99     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 2.8312 Dev= 1.95% S= 20.52 time= 1.14
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=   7.73

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     768 steps. Energy=    -531.7178471       time=       2.15
 Minus side of path:                     618 steps. Energy=    -529.1309286       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7178471  2.6783         -529.0395746 0.91354E-01     -529.1309286  11.302   9.327   8.123  13.172
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1645.7    
 decide> The unconnected minima in the chain and their distances are:
     2       10.79     4     5        7.29     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281563    
 Double-ended search iterations= 105 RMS= 2.2372 Dev= 0.33% S= 15.77 time= 0.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=   5.06

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     609 steps. Energy=    -531.5937583       time=       1.52
 Minus side of path:                     597 steps. Energy=    -531.7178471       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.5937583  8.4036         -523.1901128  8.5277         -531.7178471   5.342   4.987  19.069   5.611
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2908 Dev= 0.36% S= 7.58 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   5.89

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     577 steps. Energy=    -531.2399232       time=       1.40
 Minus side of path:                     577 steps. Energy=    -531.4282211       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.2399232 0.11288E-01     -531.2286350 0.19959         -531.4282211   4.353   4.221  13.958   7.666
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     1714.0    
 decide> The unconnected minima in the chain and their distances are:
     2        4.29     7     7        9.91     4     5        8.71     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1154 Dev= 0.05% S= 4.45 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.79

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     586 steps. Energy=    -531.7178471       time=       1.43
 Minus side of path:                     561 steps. Energy=    -531.5574421       time=       1.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7178471 0.17891         -531.5389408 0.18501E-01     -531.5574421   4.439   4.293  14.018   7.633
        Known (#7)                                              Known (#2)
 Unconnected minimum 7 found its way to F set.

 checkpair> Energies of the minima in the pair     4    7 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 4_U and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 4.2544 Dev= 3.57% S= 14.38 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=   4.98

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     667 steps. Energy=    -533.6285868       time=       1.66
 Minus side of path:                     607 steps. Energy=    -534.1270668       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.6285868  8.6495         -524.9790856  9.1480         -534.1270668   9.725   4.245  22.486   4.758
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5150 Dev= 1.33% S= 9.69 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=   3.13
 isnewts> transition state is the same as number        1 energy=     -522.7889601466
 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:                     599 steps. Energy=    -526.4092652       time=       1.48
 Minus side of path:                     594 steps. Energy=    -530.5350581       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -526.4092652  3.6203         -522.7889601  7.7461         -530.5350581   6.604   5.292  20.817   5.140
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     2047.2    
 decide> The unconnected minima in the chain and their distances are:
     6       10.92     4     5        6.21     8     9        7.96     3 
 

 tryconnect> 105-iteration DNEB run for minima 4_U and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 2.0100 Dev= 0.36% S= 15.76 time= 0.55
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   4.67

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     626 steps. Energy=    -531.7178471       time=       1.56
 Minus side of path:                     615 steps. Energy=    -531.5937583       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.7178471  4.2842         -527.4336455  4.1601         -531.5937583  17.701  11.090  11.851   9.029
        Known (#4)                                              Known (#6)
 Unconnected minimum 4 found its way to F set.

 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= 0.3416 Dev= 0.10% S= 7.38 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.78

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     668 steps. Energy=    -533.3980169       time=       1.67
 Minus side of path:                     618 steps. Energy=    -531.2399232       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3980169  7.0732         -526.3248597  4.9151         -531.2399232  10.113   6.704  15.568   6.873
        *NEW* (Placed in 12)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 3_S and 9_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2151 Dev= 0.19% S= 8.28 time= 0.29
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.62

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     580 steps. Energy=    -526.4092652       time=       1.41
 Minus side of path:                     596 steps. Energy=    -531.4282211       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -526.4092652 0.15820         -526.2510652  5.1772         -531.4282211   8.665   7.963  12.595   8.495
        Known (#3)                                              Known (#9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      1 missing connections, weight=     315.67    
 decide> The unconnected minima in the chain and their distances are:
     5        6.81    12 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2645 Dev= 0.24% S= 7.07 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     644 steps. Energy=    -533.3980169       time=       1.59
 Minus side of path:                     620 steps. Energy=    -529.1309286       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.3980169  4.3566         -529.0413961 0.89532E-01     -529.1309286   7.426   6.809   8.962  11.939
        Known (#12)                                             Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -530.5350581  7.7461        -522.7889601  3.6203        -526.4092652   6.604   5.293  20.655   5.180
  10     -526.4092652 0.15820        -526.2510652  5.1772        -531.4282211   8.665   7.963  12.595   8.495
   4     -531.4282211 0.19959        -531.2286350 0.11288E-01    -531.2399232   4.353   4.221  13.958   7.666
   9     -531.2399232  4.9151        -526.3248597  7.0732        -533.3980169  10.113   6.704  15.568   6.873
  11     -533.3980169  4.3566        -529.0413961 0.89532E-01    -529.1309286   7.426   6.809   8.962  11.939
   2     -529.1309286 0.91354E-01    -529.0395746  2.6783        -531.7178471  11.302   9.327   8.123  13.172
   8     -531.7178471  4.2842        -527.4336455  4.1601        -531.5937583  17.701  11.090  11.851   9.029
   3     -531.5937583  8.4036        -523.1901128  8.5277        -531.7178471   5.342   4.987  19.069   5.611
   5     -531.7178471 0.17891        -531.5389408 0.18501E-01    -531.5574421   4.439   4.293  14.018   7.633

 Number of TS in the path       =      9
 Number of cycles               =      6

 Elapsed time=                                86.82
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23567 time=          47.52 %= 54.7
 OPTIM> # of energy+gradient+Hessian calls=       380 time=          20.69 %= 23.8
