
 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 05/27/2012 at 17:42:37
  [-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> Constraint potential parameters read from file congeom.dat
 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.05000       10.00000
 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> Number of updates in qci=   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=    -445.9176387     RMS force=    0.9530694135E-06
 OPTIM> Final energy  =    -447.8205178     RMS force=    0.9830760254E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      35.15301422    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     42756.    
 decide> The unconnected minima in the chain and their distances are:
     2       34.93     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    62
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    282 fraction=    0.990000 images=     4 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    307 steps, energy/image=    -429.8389370     RMS=1.075973909     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   42.15     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.2981058282    
 Double-ended search iterations= 420 RMS= 0.0230 Dev= 3.48% S= 38.16 time= 37.85
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        132
 DNEB run yielded 1 true transition state(s) time=  71.51

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1548 steps. Energy=    -446.9477859       time=      19.63
 Minus side of path:                    1290 steps. Energy=    -445.7547907       time=      15.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.9477859  1.2054         -445.7423767 0.12414E-01     -445.7547907  25.232  23.819   2.829  77.062
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     4174.9    
 decide> The unconnected minima in the chain and their distances are:
     2        7.71     3     4       15.47     1 
 

 tryconnect> Interpolation for minima 2_F and 3_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   209
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     33 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     58 steps, energy/image=    -441.8564571     RMS=.2107122600     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   9.744     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.3259 Dev= 0.83% S= 8.60 time= 1.05
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  24.12

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1293 steps. Energy=    -447.8205178       time=      13.61
 Minus side of path:                    1283 steps. Energy=    -446.9477859       time=      13.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.8205178  3.9760         -443.8444892  3.1033         -446.9477859   8.910   7.718  29.436   7.406
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   152
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     67 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     92 steps, energy/image=    -440.4560792     RMS=.3108776263     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   20.01     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 210 RMS= 0.0327 Dev= 0.70% S= 15.51 time= 9.35
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=  30.65

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1757 steps. Energy=    -447.5232955       time=      21.46
 Minus side of path:                    1287 steps. Energy=    -445.7547907       time=      13.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5232955  1.7757         -445.7476194 0.71713E-02     -445.7547907  39.290  37.214   3.272  66.618
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     7430.0    
 decide> The unconnected minima in the chain and their distances are:
     4       15.47     1 
 

 tryconnect> Interpolation for minima 1_S and 4_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   152
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     67 fraction=    0.990000 images=    15 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     92 steps, energy/image=    -424.5130533     RMS=8.309888780     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   23.30     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.8803147734E-01
 Double-ended search iterations= 805 RMS= 0.0287 Dev= 1.86% S= 16.10 time= 136.81
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  23.94
 isnewts> transition state is the same as number        3 energy=     -445.7476193749
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1762 steps. Energy=    -447.5232955       time=      21.21
 Minus side of path:                    1304 steps. Energy=    -445.7547907       time=      13.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5232955  1.7757         -445.7476194 0.71713E-02     -445.7547907  39.326  37.257   3.238  67.336
        Known (#5)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     35309.    
 decide> The unconnected minima in the chain and their distances are:
     3       32.77     1 
 

 tryconnect> Interpolation for minima 1_S and 3_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    65
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    238 fraction=    0.990000 images=     4 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    263 steps, energy/image=    -437.7051973     RMS=.5061445753     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   40.51     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 420 RMS= 0.0905 Dev= 1.73% S= 34.19 time= 37.39
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         73
 DNEB run yielded 1 true transition state(s) time=  41.39
 isnewts> transition state is the same as number        1 energy=     -445.7423767003
 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:                    1289 steps. Energy=    -445.7547907       time=      14.73
 Minus side of path:                    1579 steps. Energy=    -446.9477859       time=      20.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.7547907 0.12414E-01     -445.7423767  1.2054         -446.9477859  25.231  23.816   2.832  76.982
        Known (#4)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     35923.    
 decide> The unconnected minima in the chain and their distances are:
     5       32.96     1 
 

 tryconnect> Interpolation for minima 1_S and 5_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    88
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    159 fraction=    0.990000 images=     3 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    184 steps, energy/image=    -411.4891202     RMS=6.969477064     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      1     5 dist=   39.97     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.4194648369    
 Double-ended search iterations= 385 RMS= 0.0430 Dev= 0.54% S= 35.54 time= 31.67
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=  40.80

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1319 steps. Energy=    -445.9176387       time=      17.56
 Minus side of path:                    1685 steps. Energy=    -447.5232955       time=      22.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.9176387 0.49709E-02     -445.9126678  1.6106         -447.5232955  33.891  33.118   3.847  56.666
        Known (#1)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -445.9176387 0.49709E-02    -445.9126678  1.6106        -447.5232955  33.891  33.118   3.847  56.666
   3     -447.5232955  1.7757        -445.7476194 0.71713E-02    -445.7547907  39.290  37.214   3.272  66.618
   1     -445.7547907 0.12414E-01    -445.7423767  1.2054        -446.9477859  25.232  23.819   2.829  77.062
   2     -446.9477859  3.1033        -443.8444892  3.9760        -447.8205178   8.910   7.718  29.436   7.406

 Number of TS in the path       =      4
 Number of cycles               =      5

 Elapsed time=                               702.61
 OPTIM> # of energy calls=                         12 time=           0.09 %=  0.0
 OPTIM> # of energy+gradient calls=             60249 time=         443.42 %= 63.1
 OPTIM> # of energy+gradient+Hessian calls=       350 time=          99.37 %= 14.1
