
 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 19:21:45
  [-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 = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 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    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
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>  654 Cartesian coordinates will be optimised for  218 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=    -452.4075266     RMS force=    0.9464168364E-06
 OPTIM> Final energy  =    -454.5243993     RMS force=    0.8058620959E-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=    0.23708E+06
 decide> The unconnected minima in the chain and their distances are:
     2       61.89     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1505637004    
 Double-ended search iterations= 630 RMS= 0.0473 Dev= 5.87% S= 75.41 time= 86.16
 Following    1 images are candidates for TS:    8  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 127.03
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.47415E+06
 decide> The unconnected minima in the chain and their distances are:
     2       61.89     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 805 RMS= 0.0658 Dev= 4.58% S= 69.57 time= 140.27
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        177
 DNEB run yielded 1 true transition state(s) time= 102.74

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1479 steps. Energy=    -454.1177427       time=      16.28
 Minus side of path:                    1324 steps. Energy=    -452.5039879       time=      14.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.1177427  2.0147         -452.1030514 0.40094         -452.5039879  54.267  52.500   2.160 100.925
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.17877E+06
 decide> The unconnected minima in the chain and their distances are:
     2       24.00     4     4       54.84     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 4_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1213 Dev= 2.67% S= 27.63 time= 12.77
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  38.13

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1251 steps. Energy=    -453.8648624       time=      12.86
 Minus side of path:                    1233 steps. Energy=    -454.5243993       time=      12.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8648624 0.15107         -453.7137897 0.81061         -454.5243993  12.445  12.081   4.152  52.499
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 560-iteration DNEB run for minima 1_S and 4_U using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0503 Dev= 2.36% S= 65.09 time= 66.94
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        183
 DNEB run yielded 1 true transition state(s) time=  98.93
 isnewts> transition state is the same as number        1 energy=     -452.1030514095
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1465 steps. Energy=    -454.1177427       time=      16.01
 Minus side of path:                    1333 steps. Energy=    -452.5039879       time=      13.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.1177427  2.0147         -452.1030514 0.40094         -452.5039879  54.268  52.500   2.159 100.987
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.21715E+06
 decide> The unconnected minima in the chain and their distances are:
     5       60.11     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 5_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1505637004    
 Double-ended search iterations= 630 RMS= 0.0471 Dev= 4.07% S= 70.51 time= 84.46
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        174
 DNEB run yielded 1 true transition state(s) time=  90.62

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1338 steps. Energy=    -451.7528867       time=      15.02
 Minus side of path:                    1833 steps. Energy=    -453.0557725       time=      25.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7528867 0.41414         -451.3387444  1.7170         -453.0557725  65.871  57.797   1.703 128.040
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=    0.12297E+06
 decide> The unconnected minima in the chain and their distances are:
     5       21.25     4     4       17.47     7     7       47.63     1 
 

 tryconnect> 210-iteration DNEB run for minima 4_U and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.566053647    
 Double-ended search iterations= 210 RMS= 2.2912 Dev= 1.94% S= 24.30 time= 9.54
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=  39.74

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1262 steps. Energy=    -453.1135556       time=      13.36
 Minus side of path:                    1273 steps. Energy=    -452.5039879       time=      13.17

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1135556  1.0763         -452.0372226 0.46677         -452.5039879  23.533  22.094   1.700 128.225
        *NEW* (Placed in 8)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 175-iteration DNEB run for minima 4_U and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0371 Dev= 0.11% S= 17.58 time= 6.54
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=  43.68

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1320 steps. Energy=    -453.0557725       time=      14.06
 Minus side of path:                    1298 steps. Energy=    -452.5039879       time=      13.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.0557725 0.66263         -452.3931465 0.11084         -452.5039879  20.896  17.485   1.623 134.360
        Known (#7)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 1_S and 7_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0693 Dev= 2.64% S= 55.53 time= 51.36
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        103
 DNEB run yielded 1 true transition state(s) time=  68.87
 isnewts> transition state is the same as number        1 energy=     -452.1030514102
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=    0.11890E+06
 decide> The unconnected minima in the chain and their distances are:
     5        8.94     8     6       49.07     1 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 2.5234 Dev= 1.36% S= 10.81 time= 1.06
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        196
 DNEB run yielded 1 true transition state(s) time= 108.16

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1278 steps. Energy=    -451.7120404       time=      13.10
 Minus side of path:                    1247 steps. Energy=    -453.1135556       time=      12.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7120404 0.19697E-01     -451.6923436  1.4212         -453.1135556  22.328  20.386   6.532  33.374
        *NEW* (Placed in 9)                                     Known (#8)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 1_S and 6_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.8383950223E-01
 Double-ended search iterations= 490 RMS= 0.0165 Dev= 0.85% S= 51.26 time= 51.36
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  28.05

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1517 steps. Energy=    -452.6950300       time=      16.78
 Minus side of path:                    1372 steps. Energy=    -451.7528867       time=      14.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.6950300  1.4537         -451.2412928 0.51159         -451.7528867  48.619  47.341   1.847 118.049
        *NEW* (Placed in 10)                                    Known (#6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     58805.    
 decide> The unconnected minima in the chain and their distances are:
     5        8.94     8    10       38.57     1 
 

 tryconnect> 700-iteration DNEB run for minima 5_F and 8_U using 20 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      4.581115220    
 Double-ended search iterations= 700 RMS= 0.0889 Dev= 4.70% S= 21.02 time= 103.84
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=  36.05

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1508 steps. Energy=    -453.1135556       time=      16.53
 Minus side of path:                    1338 steps. Energy=    -454.5243993       time=      14.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1135556  9.2355         -443.8780620  10.646         -454.5243993  47.524  12.543   4.606  47.331
        Known (#8)                                              Known (#2)
 Unconnected minimum 8 found its way to F set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 10_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0228 Dev= 0.23% S= 39.25 time= 31.68
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=  31.33

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1279 steps. Energy=    -452.4075266       time=      13.23
 Minus side of path:                    1366 steps. Energy=    -452.6950300       time=      14.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4075266 0.23815         -452.1693793 0.52565         -452.6950300  40.258  38.583   1.544 141.212
        Known (#1)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -452.4075266 0.23815        -452.1693793 0.52565        -452.6950300  40.258  38.583   1.544 141.212
   8     -452.6950300  1.4537        -451.2412928 0.51159        -451.7528867  48.619  47.341   1.847 118.049
   4     -451.7528867 0.41414        -451.3387444  1.7170        -453.0557725  65.871  57.797   1.703 128.040
   6     -453.0557725 0.66263        -452.3931465 0.11084        -452.5039879  20.896  17.485   1.623 134.360
   5     -452.5039879 0.46677        -452.0372226  1.0763        -453.1135556  23.533  22.094   1.700 128.225
   9     -453.1135556  9.2355        -443.8780620  10.646        -454.5243993  47.524  12.543   4.606  47.331

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

 Elapsed time=                              1756.42
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            133033 time=         987.65 %= 56.2
 OPTIM> # of energy+gradient+Hessian calls=      1404 time=         395.22 %= 22.5
