
 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 21:39:02
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 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>> Choosing internal or Cartesian coordinates for interpolation, based on max energy.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -450.7536291     RMS force=    0.9283985086E-06
 OPTIM> Final energy  =    -447.7898285     RMS force=    0.9753718272E-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=    0.21870E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.25     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= 0.0277 Dev= 4.91% S= 74.46 time= 85.92
 Following    3 images are candidates for TS:    7   12   18  
 Converged to TS (number of iterations):         35
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         33
 DNEB run yielded 2 true transition state(s) time= 203.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1291 steps. Energy=    -451.0153708       time=      13.73
 Minus side of path:                    1301 steps. Energy=    -450.7536291       time=      14.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0153708  2.2194         -448.7959600  1.9577         -450.7536291  13.837  12.072   5.465  39.892
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1393 steps. Energy=    -448.4376628       time=      15.06
 Minus side of path:                    1301 steps. Energy=    -447.7898285       time=      13.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4376628 0.65301         -447.7846528 0.51757E-02     -447.7898285  19.105  18.758   3.369  64.706
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     87172.    
 decide> The unconnected minima in the chain and their distances are:
     4       44.34     3 
 

 tryconnect> 455-iteration DNEB run for minima 3_S and 4_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1921616749    
 Double-ended search iterations= 455 RMS= 0.0684 Dev= 5.75% S= 50.89 time= 44.23
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        197
 DNEB run yielded 1 true transition state(s) time= 101.88

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1449 steps. Energy=    -449.3143586       time=      16.68
 Minus side of path:                    1525 steps. Energy=    -449.0523929       time=      18.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3143586  1.3219         -447.9924174  1.0600         -449.0523929  65.310  63.113   2.483  87.803
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     36655.    
 decide> The unconnected minima in the chain and their distances are:
     4       16.45     6     5       31.82     1 
 

 tryconnect> 140-iteration DNEB run for minima 4_F and 6_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0593 Dev= 0.03% S= 16.58 time= 4.45
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=  46.03

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1308 steps. Energy=    -448.4376628       time=      15.59
 Minus side of path:                    1353 steps. Energy=    -449.0523929       time=      17.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4376628 0.17092E-01     -448.4205712 0.63182         -449.0523929  16.702  16.456   4.993  43.659
        Known (#4)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 315-iteration DNEB run for minima 1_S and 5_F using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.5845 Dev= 3.16% S= 36.86 time= 22.09
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):         37
 Converged to TS (number of iterations):         35
 DNEB run yielded 2 true transition state(s) time=  67.04
 isnewts> transition state is the same as number        1 energy=     -448.7959599780
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1297 steps. Energy=    -451.0153708       time=      17.24
 Minus side of path:                    1304 steps. Energy=    -450.7536291       time=      17.03

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0153708  2.2194         -448.7959600  1.9577         -450.7536291  13.837  12.073   5.464  39.900
        Known (#3)                                              Known (#1)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1603 steps. Energy=    -451.9822664       time=      23.41
 Minus side of path:                    1311 steps. Energy=    -449.3143586       time=      15.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.9822664  5.6886         -446.2936804  3.0207         -449.3143586  34.345  33.452   2.282  95.518
        *NEW* (Placed in 7)                                     Known (#5)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     50743.    
 decide> The unconnected minima in the chain and their distances are:
     5       37.02     3 
 

 tryconnect> 385-iteration DNEB run for minima 3_S and 5_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0300 Dev= 4.02% S= 42.26 time= 32.70
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  29.40
 isnewts> transition state is the same as number        6 energy=     -446.2936804049
 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:                    1601 steps. Energy=    -451.9822664       time=      18.74
 Minus side of path:                    1293 steps. Energy=    -449.3143586       time=      13.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.9822664  5.6886         -446.2936804  3.0207         -449.3143586  34.346  33.452   2.282  95.536
        Known (#7)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     64409.    
 decide> The unconnected minima in the chain and their distances are:
     5       31.82     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0387 Dev= 4.68% S= 39.91 time= 141.04
 Following    2 images are candidates for TS:    8   18  
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         42
 DNEB run yielded 2 true transition state(s) time=  66.66
 isnewts> transition state is the same as number        1 energy=     -448.7959599780
 tryconnect> Will not repeat search for TS      1 same as TS      1
 isnewts> transition state is the same as number        6 energy=     -446.2936804049
 tryconnect> Will not repeat search for TS      2 same as TS      6
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     65177.    
 decide> The unconnected minima in the chain and their distances are:
     6       40.24     3 
 

 tryconnect> 420-iteration DNEB run for minima 3_S and 6_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0785 Dev= 3.43% S= 43.81 time= 38.18
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        125
 DNEB run yielded 1 true transition state(s) time=  74.70
 isnewts> transition state is the same as number        3 energy=     -447.9924173672
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 8 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1530 steps. Energy=    -449.0523929       time=      21.51
 Minus side of path:                    1436 steps. Energy=    -449.3143586       time=      21.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0523929  1.0600         -447.9924174  1.3219         -449.3143586  65.309  63.110   2.483  87.783
        Known (#6)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=    0.10149E+06
 decide> The unconnected minima in the chain and their distances are:
     5       37.02     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 5_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.7532985809    
 Double-ended search iterations= 805 RMS= 0.0296 Dev= 4.51% S= 43.98 time= 139.16
 Following    1 images are candidates for TS:   16  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  28.55
 isnewts> transition state is the same as number        6 energy=     -446.2936804049
 tryconnect> Will not repeat search for TS      1 same as TS      6
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.11112E+06
 decide> The unconnected minima in the chain and their distances are:
     6       48.08     1 
 

 tryconnect> 490-iteration DNEB run for minima 1_S and 6_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 490 RMS= 0.0334 Dev= 5.60% S= 55.07 time= 51.37
 Following    2 images are candidates for TS:    6   10  
 Converged to TS (number of iterations):         33
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        172
 DNEB run yielded 2 true transition state(s) time= 135.03
 isnewts> transition state is the same as number        1 energy=     -448.7959599780
 tryconnect> Will not repeat search for TS      1 same as TS      1
 isnewts> transition state is the same as number        3 energy=     -447.9924173671
 tryconnect> Will not repeat search for TS      2 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 7 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.13035E+06
 decide> The unconnected minima in the chain and their distances are:
     6       40.24     3 
 

 tryconnect> 805-iteration DNEB run for minima 3_S and 6_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.0302 Dev= 4.91% S= 45.90 time= 139.03
 Following    1 images are candidates for TS:   15  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  22.84

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1837 steps. Energy=    -451.0153708       time=      23.90
 Minus side of path:                    1331 steps. Energy=    -449.0523929       time=      14.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0153708  5.1449         -445.8704287  3.1820         -449.0523929  42.210  40.252   1.534 142.076
        Known (#3)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -450.7536291  1.9577        -448.7959600  2.2194        -451.0153708  13.837  12.072   5.465  39.892
   9     -451.0153708  5.1449        -445.8704287  3.1820        -449.0523929  42.210  40.252   1.534 142.076
   4     -449.0523929 0.63182        -448.4205712 0.17092E-01    -448.4376628  16.702  16.456   4.993  43.659
   2     -448.4376628 0.65301        -447.7846528 0.51757E-02    -447.7898285  19.105  18.758   3.369  64.706

 Number of TS in the path       =      4
 Number of cycles               =      9

 Elapsed time=                              1787.41
 OPTIM> # of energy calls=                        300 time=           2.22 %=  0.1
 OPTIM> # of energy+gradient calls=            140760 time=        1047.76 %= 58.6
 OPTIM> # of energy+gradient+Hessian calls=      1147 time=         333.56 %= 18.7
