
 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 05/23/2012 at 21:25:44
  [-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=    -445.3550418     RMS force=    0.9555857342E-06
 OPTIM> Final energy  =    -448.8616561     RMS force=    0.9287234171E-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=     5705.1    
 decide> The unconnected minima in the chain and their distances are:
     2       17.87     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1407 Dev= 1.10% S= 19.31 time= 6.67
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  27.91

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1274 steps. Energy=    -445.3550418       time=      15.91
 Minus side of path:                    1575 steps. Energy=    -448.8118990       time=      22.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.3550418  1.6119         -443.7431649  5.0687         -448.8118990  25.948  24.776   7.011  31.095
        Known (#1)                                              *NEW* (Placed in 3)
 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=     7636.1    
 decide> The unconnected minima in the chain and their distances are:
     2       19.69     3 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0805 Dev= 0.24% S= 20.38 time= 6.61
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  42.92

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1243 steps. Energy=    -453.7000534       time=      13.43
 Minus side of path:                    1256 steps. Energy=    -450.7336739       time=      13.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7000534  5.3796         -448.3204535  2.4132         -450.7336739  10.195   8.429  18.722  11.644
        *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      1 steps with      1 missing connections, weight=     11410.    
 decide> The unconnected minima in the chain and their distances are:
     2       17.87     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0319 Dev= 5.59% S= 28.11 time= 139.88
 Following    3 images are candidates for TS:    3   10   17  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         38
 Converged to TS (number of iterations):         20
 DNEB run yielded 3 true transition state(s) time=  79.45
 isnewts> transition state is the same as number        1 energy=     -443.7431648837
 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:                    1279 steps. Energy=    -445.3550418       time=      13.48
 Minus side of path:                    1593 steps. Energy=    -448.8118990       time=      18.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.3550418  1.6119         -443.7431649  5.0687         -448.8118990  25.951  24.781   6.977  31.244
        Known (#1)                                              Known (#3)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1366 steps. Energy=    -448.9322512       time=      15.03
 Minus side of path:                    1271 steps. Energy=    -450.6139924       time=      13.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.9322512 0.62771         -448.3045375  2.3095         -450.6139924  31.799  30.133   3.807  57.264
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1291 steps. Energy=    -448.8616561       time=      13.99
 Minus side of path:                    1272 steps. Energy=    -448.5262603       time=      13.91

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8616561  2.6556         -446.2060224  2.3202         -448.5262603  10.650   6.693  36.335   6.000
        Known (#2)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     4743.5    
 decide> The unconnected minima in the chain and their distances are:
     8       16.80     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 8_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3359 Dev= 1.01% S= 17.77 time= 6.58
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=  24.73
 isnewts> transition state is the same as number        1 energy=     -443.7431648837
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     6528.3    
 decide> The unconnected minima in the chain and their distances are:
     8       11.47     6     7       17.12     3 
 

 tryconnect> 105-iteration DNEB run for minima 6_U and 8_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0281 Dev= 0.01% S= 11.49 time= 2.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  25.56

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1276 steps. Energy=    -449.0014670       time=      13.94
 Minus side of path:                    1277 steps. Energy=    -448.5262603       time=      14.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0014670 0.58222         -448.4192424 0.10702         -448.5262603  14.452  14.219   1.988 109.651
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_S and 7_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0456 Dev= 0.11% S= 17.27 time= 6.58
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 145.25
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      3 missing connections, weight=     5929.9    
 decide> The unconnected minima in the chain and their distances are:
     9        8.03     6     7        3.87     5     4       17.50     3 
 

 tryconnect> 70-iteration DNEB run for minima 6_U and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1055 Dev= 0.00% S= 8.03 time= 1.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  27.03

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1221 steps. Energy=    -448.9322512       time=      13.77
 Minus side of path:                    1271 steps. Energy=    -449.0014670       time=      13.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.9322512 0.92214E-02     -448.9230298 0.78437E-01     -449.0014670   8.096   8.026   3.092  70.503
        Known (#6)                                              Known (#9)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 5_U and 7_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0171 Dev= 0.01% S= 3.87 time= 1.05
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=  25.29

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1248 steps. Energy=    -450.7336739       time=      12.91
 Minus side of path:                    1155 steps. Energy=    -450.6139924       time=      11.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.7336739 0.12124         -450.6124335 0.15589E-02     -450.6139924   3.913   3.865   6.191  35.212
        Known (#5)                                              Known (#7)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 3_S and 4_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1565 Dev= 0.45% S= 18.32 time= 6.54
 Following    2 images are candidates for TS:    1    3  
 Converged to TS (number of iterations):         42
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=  56.56

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1253 steps. Energy=    -450.6139924       time=      13.20
 Minus side of path:                    1247 steps. Energy=    -448.7802017       time=      13.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6139924  1.8559         -448.7580654 0.22136E-01     -448.7802017  18.158  16.695   2.448  89.064
        Known (#7)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to F set.

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1264 steps. Energy=    -453.7000534       time=      13.07
 Minus side of path:                    1281 steps. Energy=    -451.3789728       time=      13.38

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7000534  3.8627         -449.8373563  1.5416         -451.3789728   9.751   8.211  18.539  11.759
        Known (#4)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1.3743    
 decide> The unconnected minima in the chain and their distances are:
    10        1.11     3 
 

 tryconnect> 70-iteration DNEB run for minima 3_S and 10_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0243 Dev= 0.02% S= 1.11 time= 1.05
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=  18.00

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1221 steps. Energy=    -448.8118990       time=      12.49
 Minus side of path:                    1202 steps. Energy=    -448.7802017       time=      12.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.8118990 0.33926E-01     -448.7779730 0.22287E-02     -448.7802017   1.112   1.112  12.138  17.959
        Known (#3)                                              Known (#10)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -445.3550418  1.6119        -443.7431649  5.0687        -448.8118990  25.948  24.776   7.011  31.095
  11     -448.8118990 0.33926E-01    -448.7779730 0.22287E-02    -448.7802017   1.112   1.112  12.138  17.959
   9     -448.7802017 0.22136E-01    -448.7580654  1.8559        -450.6139924  18.158  16.695   2.448  89.064
   4     -450.6139924  2.3095        -448.3045375 0.62771        -448.9322512  31.799  30.133   3.807  57.264
   7     -448.9322512 0.92214E-02    -448.9230298 0.78437E-01    -449.0014670   8.096   8.026   3.092  70.503
   6     -449.0014670 0.58222        -448.4192424 0.10702        -448.5262603  14.452  14.219   1.988 109.651
   5     -448.5262603  2.3202        -446.2060224  2.6556        -448.8616561  10.650   6.693  36.335   6.000

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

 Elapsed time=                               963.28
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             70224 time=         526.41 %= 54.6
 OPTIM> # of energy+gradient+Hessian calls=       594 time=         176.28 %= 18.3
