
 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 05/28/2012 at 09:27:32
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    107
 keyword> 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=    17
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  321 Cartesian coordinates will be optimised for  107 AMBER atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 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:         0.10000       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=    -529.9237080     RMS force=    0.9228431285E-06
 OPTIM> Final energy  =    -529.0176031     RMS force=    0.8959408106E-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      14.19892004    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2039.3    
 decide> The unconnected minima in the chain and their distances are:
     2       12.67     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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    103 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    128 steps, energy/image=    -518.0743581     RMS=1.599061360     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   18.21     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 175 RMS= 0.2261 Dev= 1.44% S= 15.77 time= 1.80
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=   6.08

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     684 steps. Energy=    -527.4787619       time=       1.71
 Minus side of path:                     701 steps. Energy=    -523.8558792       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.4787619  3.6512         -523.8275988 0.28280E-01     -523.8558792  12.571  10.071   3.260  32.826
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    13   23 from     0.41743E-01 to     0.41808E-01 ref=     3.2380    
 checkperc> Increasing con cutoff atoms    26   36 from     0.48250E-02 to     0.50443E-02 ref=     1.5490    
 checkperc> Increasing con cutoff atoms    26   40 from     0.16003E-01 to     0.25821E-01 ref=     3.8885    
 checkperc> Increasing con cutoff atoms    26   41 from     0.87712E-01 to     0.12111     ref=     4.1820    
 checkperc> Increasing con cutoff atoms    36   40 from     0.18838E-01 to     0.25239E-01 ref=     2.4948    
 checkperc> Increasing con cutoff atoms    38   41 from     0.21083E-01 to     0.22532E-01 ref=     2.1014    
 checkperc> Increasing con cutoff atoms    40   43 from     0.15388E-01 to     0.19353E-01 ref=     2.1618    
 checkperc> Increasing con cutoff atoms    41   45 from     0.14710     to     0.17717     ref=     2.7767    
 checkperc> Increasing con cutoff atoms    45   48 from     0.42879E-02 to     0.49990E-02 ref=     1.5324    
 checkperc> Increasing con cutoff atoms    45   50 from     0.10815E-01 to     0.33498E-01 ref=     2.4571    
 checkperc> Increasing con cutoff atoms    45   51 from     0.96671E-02 to     0.23485E-01 ref=     3.3764    
 checkperc> Increasing con cutoff atoms    45   52 from     0.39751E-01 to     0.82060E-01 ref=     2.6116    
 checkperc> Increasing con cutoff atoms    48   50 from     0.22960E-02 to     0.40505E-02 ref=     1.3181    
 checkperc> Increasing con cutoff atoms    48   52 from     0.16304E-01 to     0.20824E-01 ref=     2.0282    
 checkperc> Increasing con cutoff atoms    49   50 from     0.55517E-02 to     0.96986E-02 ref=     2.1926    
 checkperc> Increasing con cutoff atoms    49   51 from     0.18136E-01 to     0.30744E-01 ref=     2.4017    
 checkperc> Increasing con cutoff atoms    51   52 from     0.87231E-02 to     0.11800E-01 ref=     1.7607    
 checkperc> Increasing con cutoff atoms    97   98 from     0.44772E-02 to     0.46758E-02 ref=     2.1625    
 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=     1721.1    
 decide> The unconnected minima in the chain and their distances are:
     2        9.70     4     3        9.29     1 
 

 tryconnect> Interpolation for minima 2_F and 4_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=    91
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     61 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     86 steps, energy/image=    -519.0230131     RMS=.9006935626     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   11.17     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.3258 Dev= 0.93% S= 10.62 time= 0.65
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   8.61

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     707 steps. Energy=    -530.1667564       time=       1.77
 Minus side of path:                     656 steps. Energy=    -523.8558792       time=       1.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1667564  6.4659         -523.7008263 0.15505         -523.8558792  15.652  11.385   7.458  14.346
        *NEW* (Placed in 5)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    40   42 from     0.43420E-02 to     0.43847E-02 ref=     1.5443    
 checkperc> Increasing con cutoff atoms    43   44 from     0.13499E-01 to     0.13876E-01 ref=     1.7573    
 checkperc> Increasing con cutoff atoms    46   47 from     0.10008E-01 to     0.10704E-01 ref=     1.7564    
 checkperc> Increasing con cutoff atoms    48   49 from     0.17878E-02 to     0.19012E-02 ref=     1.2263    
 checkperc> Increasing con cutoff atoms    74   88 from     0.38325E-01 to     0.38810E-01 ref=     3.8815    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S 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=    91
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     90 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    115 steps, energy/image=    -522.4501909     RMS=.4302066108     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   11.70     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2189 Dev= 0.71% S= 11.28 time= 0.65
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        193
 DNEB run yielded 1 true transition state(s) time=  20.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     678 steps. Energy=    -530.6696097       time=       1.70
 Minus side of path:                     646 steps. Energy=    -529.8075484       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.6696097  1.4957         -529.1739444 0.63360         -529.8075484  19.300  17.194   2.003  53.415
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms     9   12 from     0.26429E-01 to     0.26929E-01 ref=     2.8434    
 checkperc> Increasing con cutoff atoms    12   13 from     0.30841E-03 to     0.32389E-03 ref=     1.0918    
 checkperc> Increasing con cutoff atoms    13   14 from     0.11081E-01 to     0.16349E-01 ref=     2.1481    
 checkperc> Increasing con cutoff atoms    36   41 from     0.99677E-01 to     0.11209     ref=     2.6963    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      3 missing connections, weight=     2506.7    
 decide> The unconnected minima in the chain and their distances are:
     2        9.70     4     3        8.37     7     7        4.41     1 
 

 tryconnect> Interpolation for minima 2_F and 4_U 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=    91
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     88 fraction=    0.990000 images=    15 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    113 steps, energy/image=    -512.5666604     RMS=3.581554771     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   15.80     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.0544 Dev= 5.48% S= 15.12 time= 37.87
 Following    2 images are candidates for TS:   12   21  
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         32
 DNEB run yielded 2 true transition state(s) time=   8.15
 isnewts> transition state is the same as number        1 energy=     -523.8275988348
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     746 steps. Energy=    -529.9237080       time=       1.92
 Minus side of path:                     649 steps. Energy=    -529.0176031       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.9237080  4.1581         -525.7656044  3.2520         -529.0176031  20.353  12.876  10.517  10.174
        Known (#1)                                              Known (#2)

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     684 steps. Energy=    -527.4787619       time=       1.69
 Minus side of path:                     711 steps. Energy=    -523.8558792       time=       1.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -527.4787619  3.6512         -523.8275988 0.28280E-01     -523.8558792  12.572  10.071   3.253  32.895
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 3_U and 7_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=    97
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    115 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    140 steps, energy/image=    -521.0419598     RMS=.5138724518     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   11.73     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 0.7973 Dev= 1.70% S= 10.38 time= 0.65
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.71

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     707 steps. Energy=    -529.8075484       time=       1.76
 Minus side of path:                     637 steps. Energy=    -527.4787619       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8075484  2.3446         -527.4629505 0.15811E-01     -527.4787619   9.294   8.423  16.278   6.573
        Known (#7)                                              Known (#3)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 7_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=   103
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     35 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     60 steps, energy/image=    -522.8580168     RMS=3.579585565     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      1     7 dist=   12.99     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      27.85962590    
 Double-ended search iterations= 105 RMS= 1.1035 Dev= 13.34% S= 4.65 time= 0.65
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.26

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     631 steps. Energy=    -529.9237080       time=       1.53
 Minus side of path:                     622 steps. Energy=    -529.8075484       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.9237080 0.19922         -529.7244867 0.83062E-01     -529.8075484   4.891   4.411  23.762   4.503
        Known (#1)                                              Known (#7)
 Unconnected minimum 7 found its way to S set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -529.9237080  4.1581        -525.7656044  3.2520        -529.0176031  20.353  12.876  10.517  10.174

 Number of TS in the path       =      1
 Number of cycles               =      3

 Elapsed time=                               119.24
 OPTIM> # of energy calls=                         12 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             36962 time=          73.81 %= 61.9
 OPTIM> # of energy+gradient+Hessian calls=       454 time=          24.56 %= 20.6
