
 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 22:10:10
  [-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:         0.10000       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=    -448.4521141     RMS force=    0.9731429795E-06
 OPTIM> Final energy  =    -443.7475080     RMS force=    0.9145887768E-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      392.0249025    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     27324.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.73     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=   137
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    204 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    229 steps, energy/image=    -430.6309457     RMS=.7414109967     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   38.31     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0379 Dev= 2.36% S= 41.54 time= 31.92
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        209
 DNEB run yielded 1 true transition state(s) time= 127.45

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1314 steps. Energy=    -448.6436502       time=      13.93
 Minus side of path:                    1286 steps. Energy=    -448.5798885       time=      13.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6436502 0.73795         -447.9057045 0.67418         -448.5798885  29.363  25.128   2.385  91.411
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    43   48 from     0.11668E-01 to     0.11711E-01 ref=     2.0495    
 checkperc> Increasing con cutoff atoms    45   46 from     0.49061E-02 to     0.49156E-02 ref=     1.7653    
 checkperc> Increasing con cutoff atoms    60   62 from     0.14386E-02 to     0.15272E-02 ref=     1.3803    
 checkperc> Increasing con cutoff atoms    60   65 from     0.38903E-02 to     0.45604E-02 ref=     3.6622    
 checkperc> Increasing con cutoff atoms    60   66 from     0.71061E-02 to     0.77580E-02 ref=     4.1932    
 checkperc> Increasing con cutoff atoms    60   67 from     0.13104E-02 to     0.16059E-02 ref=     4.6475    
 checkperc> Increasing con cutoff atoms    60   68 from     0.18736E-02 to     0.20089E-02 ref=     5.6719    
 checkperc> Increasing con cutoff atoms    61   62 from     0.28405E-02 to     0.34129E-02 ref=     2.1920    
 checkperc> Increasing con cutoff atoms    61   64 from     0.31307E-02 to     0.34811E-02 ref=     3.3175    
 checkperc> Increasing con cutoff atoms    61   65 from     0.53697E-02 to     0.67284E-02 ref=     4.6640    
 checkperc> Increasing con cutoff atoms    61   66 from     0.98442E-02 to     0.11799E-01 ref=     5.0783    
 checkperc> Increasing con cutoff atoms    61   67 from     0.19833E-02 to     0.23514E-02 ref=     5.7141    
 checkperc> Increasing con cutoff atoms    61   68 from     0.31863E-02 to     0.36765E-02 ref=     6.7229    
 checkperc> Increasing con cutoff atoms    61   72 from     0.17114E-01 to     0.18894E-01 ref=     5.1387    
 checkperc> Increasing con cutoff atoms    62   64 from     0.13128E-02 to     0.17647E-02 ref=     1.3782    
 checkperc> Increasing con cutoff atoms    62   65 from     0.45912E-02 to     0.55869E-02 ref=     2.5497    
 checkperc> Increasing con cutoff atoms    62   66 from     0.75778E-02 to     0.76432E-02 ref=     2.8872    
 checkperc> Increasing con cutoff atoms    62   67 from     0.33874E-02 to     0.44322E-02 ref=     3.7627    
 checkperc> Increasing con cutoff atoms    62   68 from     0.41838E-02 to     0.51083E-02 ref=     4.6863    
 checkperc> Increasing con cutoff atoms    62   69 from     0.29507E-02 to     0.33174E-02 ref=     4.1392    
 checkperc> Increasing con cutoff atoms    64   65 from     0.37725E-03 to     0.64704E-03 ref=     1.4035    
 checkperc> Increasing con cutoff atoms    64   67 from     0.74111E-03 to     0.89937E-03 ref=     2.4220    
 checkperc> Increasing con cutoff atoms    65   67 from     0.88002E-03 to     0.10548E-02 ref=     1.4045    
 checkperc> Increasing con cutoff atoms    67   68 from     0.15316E-03 to     0.28339E-03 ref=     1.0826    
 checkperc> Increasing con cutoff atoms    67   69 from     0.71769E-03 to     0.74375E-03 ref=     1.4061    
 checkperc> Increasing con cutoff atoms    69   70 from     0.18316E-03 to     0.53989E-03 ref=     1.0823    
 checkperc> Increasing con cutoff atoms    70   73 from     0.24113E-02 to     0.28970E-02 ref=     3.4345    
 checkperc> Increasing con cutoff atoms    72   73 from     0.46475E-02 to     0.51111E-02 ref=     2.1601    
 checkperc> Increasing con cutoff atoms    78   90 from     0.11560E-01 to     0.12373E-01 ref=     2.4169    
 checkperc> Increasing con cutoff atoms   113  115 from     0.74760E-01 to     0.75790E-01 ref=     2.9282    
 checkperc> Increasing con cutoff atoms   136  139 from     0.18770E-01 to     0.18968E-01 ref=     2.1502    
 checkperc> Increasing con cutoff atoms   142  150 from     0.44264E-02 to     0.50969E-02 ref=     5.6710    
 checkperc> Increasing con cutoff atoms   149  150 from     0.12835E-02 to     0.17959E-02 ref=     1.0818    
 checkperc> Increasing con cutoff atoms   172  176 from     0.27698E-01 to     0.27888E-01 ref=     2.4500    
 checkperc> Increasing con cutoff atoms    40   44 from     0.24036E-01 to     0.24306E-01 ref=     2.5513    
 checkperc> Increasing con cutoff atoms    40   45 from     0.17662E-01 to     0.17732E-01 ref=     3.4881    
 checkperc> Increasing con cutoff atoms    40   53 from     0.34873E-01 to     0.39181E-01 ref=     2.5450    
 checkperc> Increasing con cutoff atoms    43   48 from     0.11711E-01 to     0.12126E-01 ref=     2.0495    
 checkperc> Increasing con cutoff atoms    45   46 from     0.49156E-02 to     0.49255E-02 ref=     1.7653    
 checkperc> Increasing con cutoff atoms    50   53 from     0.11977E-01 to     0.13633E-01 ref=     2.0114    
 checkperc> Increasing con cutoff atoms    51   52 from     0.93742E-02 to     0.95872E-02 ref=     2.2539    
 checkperc> Increasing con cutoff atoms    51   54 from     0.51394E-01 to     0.57801E-01 ref=     2.8632    
 checkperc> Increasing con cutoff atoms    56   58 from     0.79223E-03 to     0.14704E-02 ref=     1.0906    
 checkperc> Increasing con cutoff atoms    60   67 from     0.16059E-02 to     0.19838E-02 ref=     4.6475    
 checkperc> Increasing con cutoff atoms    60   68 from     0.20089E-02 to     0.20456E-02 ref=     5.6719    
 checkperc> Increasing con cutoff atoms    60   69 from     0.18361E-02 to     0.20227E-02 ref=     4.6358    
 checkperc> Increasing con cutoff atoms    78   90 from     0.12373E-01 to     0.16007E-01 ref=     2.4169    
 checkperc> Increasing con cutoff atoms    80   85 from     0.68535E-02 to     0.73712E-02 ref=     2.1573    
 checkperc> Increasing con cutoff atoms   141  151 from     0.12941E-01 to     0.13133E-01 ref=     3.8934    
 checkperc> Increasing con cutoff atoms   141  152 from     0.14406E-01 to     0.14505E-01 ref=     4.8034    
 checkperc> Increasing con cutoff atoms   142  151 from     0.50028E-02 to     0.53448E-02 ref=     4.6342    
 checkperc> Increasing con cutoff atoms   144  145 from     0.57882E-02 to     0.58724E-02 ref=     1.0189    
 checkperc> Increasing con cutoff atoms   144  151 from     0.68338E-02 to     0.69923E-02 ref=     4.1402    
 checkperc> Increasing con cutoff atoms   144  152 from     0.70025E-02 to     0.85783E-02 ref=     5.2193    
 checkperc> Increasing con cutoff atoms   145  146 from     0.11344E-01 to     0.11705E-01 ref=     2.1372    
 checkperc> Increasing con cutoff atoms   145  153 from     0.11743E-01 to     0.13111E-01 ref=     4.4799    
 checkperc> Increasing con cutoff atoms   145  154 from     0.10430E-01 to     0.12068E-01 ref=     5.3623    
 checkperc> Increasing con cutoff atoms   145  155 from     0.85714E-02 to     0.10171E-01 ref=     3.2096    
 checkperc> Increasing con cutoff atoms   146  149 from     0.31419E-02 to     0.32851E-02 ref=     2.4225    
 checkperc> Increasing con cutoff atoms   151  153 from     0.16456E-02 to     0.17134E-02 ref=     1.4081    
 checkperc> Increasing con cutoff atoms   151  155 from     0.51105E-02 to     0.67541E-02 ref=     2.4604    
 checkperc> Increasing con cutoff atoms   152  155 from     0.48176E-02 to     0.69407E-02 ref=     3.4330    
 checkperc> Increasing con cutoff atoms   172  176 from     0.27888E-01 to     0.40496E-01 ref=     2.4500    
 checkperc> Increasing con cutoff atoms   174  176 from     0.66696E-02 to     0.79550E-02 ref=     1.5376    
 checkperc> Increasing con cutoff atoms   179  186 from     0.40232E-02 to     0.45675E-02 ref=     4.5043    
 checkperc> Increasing con cutoff atoms   180  190 from     0.34677E-02 to     0.38839E-02 ref=     5.6556    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     54648.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.73     1 
 

 tryconnect> Interpolation for minima 1_S and 2_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=   137
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    296 fraction=    0.990000 images=    17 time=       1.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    321 steps, energy/image=    -419.9455188     RMS=1.901550452     images=  17
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   78.44     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0738 Dev= 3.40% S= 41.57 time= 139.28
 Following    2 images are candidates for TS:   12   23  
 Converged to TS (number of iterations):         54
 Converged to TS (number of iterations):         28
 DNEB run yielded 2 true transition state(s) time=  70.09

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1358 steps. Energy=    -447.5490106       time=      16.91
 Minus side of path:                    1338 steps. Energy=    -448.4521141       time=      16.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5490106  5.3542         -442.1948353  6.2573         -448.4521141  28.139  19.228   9.831  22.175
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1309 steps. Energy=    -443.7475080       time=      15.79
 Minus side of path:                    1402 steps. Energy=    -447.5490106       time=      17.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.7475080 0.43934E-01     -443.7035743  3.8454         -447.5490106  21.665  18.029   5.184  42.050
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -448.4521141  6.2573        -442.1948353  5.3542        -447.5490106  28.139  19.228   9.831  22.175
   3     -447.5490106  3.8454        -443.7035743 0.43934E-01    -443.7475080  21.665  18.029   5.184  42.050

 Number of TS in the path       =      2
 Number of cycles               =      2

 Elapsed time=                               468.64
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=             36195 time=         269.44 %= 57.5
 OPTIM> # of energy+gradient+Hessian calls=       291 time=          89.08 %= 19.0
