
 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 22:13:23
  [-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=    -445.2490701     RMS force=    0.9988529171E-06
 OPTIM> Final energy  =    -452.9040418     RMS force=    0.9334270934E-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      58.28199650    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     85409.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.98     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=    29
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    388 fraction=    0.990000 images=     4 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    413 steps, energy/image=    -390.7345759     RMS=7.638936077     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   46.81     Attempts, images and iterations=     0    14   490
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 490 RMS= 0.0928 Dev= 6.05% S= 56.03 time= 51.69
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=  43.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1299 steps. Energy=    -445.2490701       time=      14.14
 Minus side of path:                    1288 steps. Energy=    -444.8967190       time=      14.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2490701  2.7566         -442.4924805  2.4042         -444.8967190  14.484  11.490  16.564  13.161
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms   145  153 from     0.11743E-01 to     0.11944E-01 ref=     4.4799    
 checkperc> Increasing con cutoff atoms   160  172 from     0.26697E-01 to     0.26882E-01 ref=     2.4540    
 checkperc> Increasing con cutoff atoms   160  173 from     0.46000E-01 to     0.47427E-01 ref=     2.5620    
 checkperc> Increasing con cutoff atoms   171  174 from     0.45072E-01 to     0.48335E-01 ref=     2.8556    
 checkperc> Increasing con cutoff atoms   172  175 from     0.18181E-01 to     0.20608E-01 ref=     2.0859    
 checkperc> Increasing con cutoff atoms   174  175 from     0.93399E-03 to     0.94569E-03 ref=     1.0911    
 checkperc> Increasing con cutoff atoms   174  178 from     0.20529E-01 to     0.21889E-01 ref=     2.1464    
 checkperc> Increasing con cutoff atoms   175  176 from     0.18027E-01 to     0.18319E-01 ref=     2.1365    
 checkperc> Increasing con cutoff atoms   176  179 from     0.56944E-02 to     0.57250E-02 ref=     1.5025    
 checkperc> Increasing con cutoff atoms   176  184 from     0.16957E-01 to     0.17018E-01 ref=     3.8213    
 checkperc> Increasing con cutoff atoms   176  186 from     0.16856E-01 to     0.16983E-01 ref=     5.9810    
 checkperc> Increasing con cutoff atoms   179  182 from     0.35010E-02 to     0.36416E-02 ref=     2.2381    
 checkperc> Increasing con cutoff atoms   179  184 from     0.41171E-02 to     0.42589E-02 ref=     2.3488    
 checkperc> Increasing con cutoff atoms   179  185 from     0.61418E-02 to     0.62835E-02 ref=     3.6935    
 checkperc> Increasing con cutoff atoms   179  186 from     0.40232E-02 to     0.41211E-02 ref=     4.5043    
 checkperc> Increasing con cutoff atoms   179  188 from     0.10217E-01 to     0.10222E-01 ref=     5.3789    
 checkperc> Increasing con cutoff atoms   182  189 from     0.38233E-02 to     0.38721E-02 ref=     4.1389    
 checkperc> Increasing con cutoff atoms   182  190 from     0.45657E-02 to     0.46807E-02 ref=     5.2177    
 checkperc> Increasing con cutoff atoms   183  190 from     0.99458E-02 to     0.99620E-02 ref=     5.9822    
 checkperc> Increasing con cutoff atoms   184  189 from     0.38197E-02 to     0.38448E-02 ref=     2.7866    
 checkperc> Increasing con cutoff atoms   184  190 from     0.45352E-02 to     0.46529E-02 ref=     3.8682    
 checkperc> Increasing con cutoff atoms   184  191 from     0.52173E-02 to     0.52818E-02 ref=     2.4176    
 checkperc> Increasing con cutoff atoms   184  192 from     0.53298E-02 to     0.57262E-02 ref=     3.4033    
 checkperc> Increasing con cutoff atoms   185  190 from     0.38828E-02 to     0.40525E-02 ref=     3.4097    
 checkperc> Increasing con cutoff atoms   185  192 from     0.75009E-02 to     0.75246E-02 ref=     3.8967    
 checkperc> Increasing con cutoff atoms   185  193 from     0.49424E-02 to     0.49804E-02 ref=     2.4852    
 checkperc> Increasing con cutoff atoms   186  190 from     0.38350E-02 to     0.40112E-02 ref=     4.3091    
 checkperc> Increasing con cutoff atoms   186  192 from     0.75647E-02 to     0.75803E-02 ref=     4.9776    
 checkperc> Increasing con cutoff atoms   186  193 from     0.36211E-02 to     0.36724E-02 ref=     3.4584    
 checkperc> Increasing con cutoff atoms   187  189 from     0.87671E-03 to     0.89825E-03 ref=     1.4061    
 checkperc> Increasing con cutoff atoms   189  190 from     0.69854E-03 to     0.80138E-03 ref=     1.0819    
 checkperc> Increasing con cutoff atoms   191  192 from     0.28892E-02 to     0.29529E-02 ref=     1.0784    
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     83558.    
 decide> The unconnected minima in the chain and their distances are:
     2       43.67     3 
 

 tryconnect> Interpolation for minima 2_F and 3_S 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=    21
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    361 fraction=    0.990000 images=     4 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    386 steps, energy/image=    -434.7756620     RMS=1.126138259     images=   5
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   44.79     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0475 Dev= 3.40% S= 51.01 time= 44.53
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=  31.55

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1532 steps. Energy=    -445.2769992       time=      18.76
 Minus side of path:                    1301 steps. Energy=    -449.2587913       time=      14.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2769992  2.7342         -442.5427957  6.7160         -449.2587913  60.940  53.574   4.693  46.453
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms   161  170 from     0.19726E-01 to     0.19733E-01 ref=     2.1223    
 checkperc> Increasing con cutoff atoms   171  172 from     0.87377E-02 to     0.87441E-02 ref=     2.2550    
 checkperc> Increasing con cutoff atoms   180  191 from     0.49267E-02 to     0.55669E-02 ref=     3.6467    
 checkperc> Increasing con cutoff atoms   180  192 from     0.14318E-01 to     0.15336E-01 ref=     4.1942    
 checkperc> Increasing con cutoff atoms   182  192 from     0.83381E-02 to     0.10107E-01 ref=     4.3768    
 checkperc> Increasing con cutoff atoms   183  192 from     0.72698E-02 to     0.93380E-02 ref=     5.3574    
 checkperc> Increasing con cutoff atoms   184  193 from     0.17505E-02 to     0.17532E-02 ref=     1.4292    
 checkperc> Increasing con cutoff atoms   187  191 from     0.15725E-02 to     0.38423E-02 ref=     2.4446    
 checkperc> Increasing con cutoff atoms   188  191 from     0.30938E-02 to     0.40109E-02 ref=     3.4231    
 checkperc> Increasing con cutoff atoms   189  191 from     0.82330E-03 to     0.14933E-02 ref=     1.4089    
 checkperc> Increasing con cutoff atoms   156  160 from     0.32904E-01 to     0.33326E-01 ref=     2.5188    
 checkperc> Increasing con cutoff atoms   176  177 from     0.20138E-02 to     0.20458E-02 ref=     1.0898    
 checkperc> Increasing con cutoff atoms   194  195 from     0.20925E-02 to     0.26047E-02 ref=     1.2355    
 checkperc> Increasing con cutoff atoms   195  197 from     0.74865E-02 to     0.77250E-02 ref=     3.1388    
 checkperc> Increasing con cutoff atoms   198  199 from     0.16460E-02 to     0.20582E-02 ref=     1.0886    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     31872.    
 decide> The unconnected minima in the chain and their distances are:
     2       15.60     5     4       30.36     3 
 

 tryconnect> Interpolation for minima 2_F and 5_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=   128
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     91 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    116 steps, energy/image=    -427.9962898     RMS=6.869174302     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   20.31     Attempts, images and iterations=     0     6   210
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 210 RMS= 0.1425 Dev= 0.60% S= 16.04 time= 9.46
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=  29.96

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1276 steps. Energy=    -452.9040418       time=      14.29
 Minus side of path:                    1290 steps. Energy=    -449.2587913       time=      13.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9040418  3.7836         -449.1204617 0.13833         -449.2587913  17.514  15.598   1.951 111.720
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 3_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=   103
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    208 fraction=    0.990000 images=     5 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    233 steps, energy/image=    -432.0396269     RMS=.4782340120     images=   6
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      3     4 dist=   46.19     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 455 RMS= 0.0425 Dev= 1.39% S= 32.39 time= 44.38
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=  47.23

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1578 steps. Energy=    -445.2769992       time=      18.40
 Minus side of path:                    1373 steps. Energy=    -444.8967190       time=      14.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2769992  1.9425         -443.3344841  1.5622         -444.8967190  49.539  31.835   4.219  51.676
        Known (#4)                                              Known (#3)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -445.2490701  2.7566        -442.4924805  2.4042        -444.8967190  14.484  11.490  16.564  13.161
   4     -444.8967190  1.5622        -443.3344841  1.9425        -445.2769992  49.539  31.835   4.219  51.676
   2     -445.2769992  2.7342        -442.5427957  6.7160        -449.2587913  60.940  53.574   4.693  46.453
   3     -449.2587913 0.13833        -449.1204617  3.7836        -452.9040418  17.514  15.598   1.951 111.720

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                               432.27
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             36832 time=         274.61 %= 63.5
 OPTIM> # of energy+gradient+Hessian calls=       222 time=          62.56 %= 14.5
