
 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 22:10:01
  [-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=    -446.0492388     RMS force=    0.8369807129E-06
 OPTIM> Final energy  =    -447.1095793     RMS force=    0.9684724018E-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

 checkperc> Increasing con cutoff atoms   143  155 from     0.56294E-02 to     0.58908E-02 ref=     3.2969    
 checkperc> Increasing con cutoff atoms   174  179 from     0.46639E-01 to     0.48678E-01 ref=     2.5925    
 checkperc> Increasing con cutoff atoms   175  176 from     0.19575E-01 to     0.19581E-01 ref=     2.1377    
 checkperc> Increasing con cutoff atoms   176  179 from     0.54590E-02 to     0.56039E-02 ref=     1.5027    
 checkperc> Increasing con cutoff atoms   176  180 from     0.21564E-01 to     0.22767E-01 ref=     2.5356    
 checkperc> Increasing con cutoff atoms   176  181 from     0.41322E-01 to     0.43657E-01 ref=     2.8567    
 checkperc> Increasing con cutoff atoms   176  183 from     0.14853E-01 to     0.15609E-01 ref=     4.5981    
 checkperc> Increasing con cutoff atoms   176  184 from     0.16348E-01 to     0.17021E-01 ref=     3.8216    
 checkperc> Increasing con cutoff atoms   176  185 from     0.25219E-01 to     0.26331E-01 ref=     5.1140    
 checkperc> Increasing con cutoff atoms   176  186 from     0.15903E-01 to     0.17311E-01 ref=     5.9809    
 checkperc> Increasing con cutoff atoms   176  187 from     0.42725E-01 to     0.45182E-01 ref=     5.5241    
 checkperc> Increasing con cutoff atoms   176  188 from     0.43423E-01 to     0.45895E-01 ref=     6.6014    
 checkperc> Increasing con cutoff atoms   176  189 from     0.56063E-01 to     0.60040E-01 ref=     4.8274    
 checkperc> Increasing con cutoff atoms   176  190 from     0.63093E-01 to     0.67763E-01 ref=     5.5530    
 checkperc> Increasing con cutoff atoms   176  191 from     0.58837E-01 to     0.63000E-01 ref=     3.4373    
 checkperc> Increasing con cutoff atoms   176  192 from     0.77950E-01 to     0.84471E-01 ref=     3.2657    
 checkperc> Increasing con cutoff atoms   176  193 from     0.29115E-01 to     0.30860E-01 ref=     2.6926    
 checkperc> Increasing con cutoff atoms   179  182 from     0.35284E-02 to     0.36453E-02 ref=     2.2381    
 checkperc> Increasing con cutoff atoms   179  183 from     0.31420E-02 to     0.33216E-02 ref=     3.2006    
 checkperc> Increasing con cutoff atoms   179  184 from     0.39546E-02 to     0.40951E-02 ref=     2.3490    
 checkperc> Increasing con cutoff atoms   179  185 from     0.59724E-02 to     0.61651E-02 ref=     3.6936    
 checkperc> Increasing con cutoff atoms   179  186 from     0.36157E-02 to     0.36217E-02 ref=     4.5048    
 checkperc> Increasing con cutoff atoms   179  187 from     0.10908E-01 to     0.11509E-01 ref=     4.2988    
 checkperc> Increasing con cutoff atoms   179  188 from     0.10546E-01 to     0.10872E-01 ref=     5.3784    
 checkperc> Increasing con cutoff atoms   179  189 from     0.11936E-01 to     0.13259E-01 ref=     3.8945    
 checkperc> Increasing con cutoff atoms   179  190 from     0.12082E-01 to     0.13644E-01 ref=     4.8042    
 checkperc> Increasing con cutoff atoms   179  191 from     0.11983E-01 to     0.13202E-01 ref=     2.6633    
 checkperc> Increasing con cutoff atoms   179  192 from     0.19360E-01 to     0.21672E-01 ref=     2.9810    
 checkperc> Increasing con cutoff atoms   179  193 from     0.52326E-02 to     0.56252E-02 ref=     1.4674    
 checkperc> Increasing con cutoff atoms   180  182 from     0.19499E-02 to     0.20536E-02 ref=     1.3801    
 checkperc> Increasing con cutoff atoms   180  184 from     0.40013E-02 to     0.41650E-02 ref=     2.2809    
 checkperc> Increasing con cutoff atoms   180  185 from     0.57441E-02 to     0.59874E-02 ref=     3.6623    
 checkperc> Increasing con cutoff atoms   180  188 from     0.35120E-02 to     0.42312E-02 ref=     5.6712    
 checkperc> Increasing con cutoff atoms   180  189 from     0.26411E-02 to     0.33207E-02 ref=     4.6350    
 checkperc> Increasing con cutoff atoms   180  191 from     0.45775E-02 to     0.51633E-02 ref=     3.6464    
 checkperc> Increasing con cutoff atoms   181  182 from     0.40071E-02 to     0.41363E-02 ref=     2.1916    
 checkperc> Increasing con cutoff atoms   181  184 from     0.48987E-02 to     0.50853E-02 ref=     3.3177    
 checkperc> Increasing con cutoff atoms   181  185 from     0.80383E-02 to     0.83550E-02 ref=     4.6640    
 checkperc> Increasing con cutoff atoms   181  188 from     0.55296E-02 to     0.64091E-02 ref=     6.7220    
 checkperc> Increasing con cutoff atoms   181  189 from     0.46886E-02 to     0.53928E-02 ref=     5.7138    
 checkperc> Increasing con cutoff atoms   181  190 from     0.48945E-02 to     0.52779E-02 ref=     6.7261    
 checkperc> Increasing con cutoff atoms   181  191 from     0.69538E-02 to     0.76557E-02 ref=     4.6812    
 checkperc> Increasing con cutoff atoms   181  192 from     0.16890E-01 to     0.18894E-01 ref=     5.1345    
 checkperc> Increasing con cutoff atoms   181  193 from     0.38881E-02 to     0.41029E-02 ref=     3.2984    
 checkperc> Increasing con cutoff atoms   182  185 from     0.69157E-02 to     0.71398E-02 ref=     2.5500    
 checkperc> Increasing con cutoff atoms   182  187 from     0.52311E-02 to     0.54735E-02 ref=     3.7631    
 checkperc> Increasing con cutoff atoms   182  188 from     0.70369E-02 to     0.82302E-02 ref=     4.6852    
 checkperc> Increasing con cutoff atoms   182  193 from     0.40792E-02 to     0.43231E-02 ref=     2.2183    
 checkperc> Increasing con cutoff atoms   183  185 from     0.14589E-01 to     0.15237E-01 ref=     2.9292    
 checkperc> Increasing con cutoff atoms   183  187 from     0.13615E-01 to     0.14413E-01 ref=     4.2887    
 checkperc> Increasing con cutoff atoms   183  188 from     0.16642E-01 to     0.18711E-01 ref=     5.0762    
 checkperc> Increasing con cutoff atoms   183  189 from     0.11284E-01 to     0.11528E-01 ref=     4.9053    
 checkperc> Increasing con cutoff atoms   183  190 from     0.11918E-01 to     0.11937E-01 ref=     5.9841    
 checkperc> Increasing con cutoff atoms   184  191 from     0.52340E-02 to     0.56224E-02 ref=     2.4179    
 checkperc> Increasing con cutoff atoms   184  192 from     0.53922E-02 to     0.56299E-02 ref=     3.4034    
 checkperc> Increasing con cutoff atoms   184  193 from     0.18121E-02 to     0.19310E-02 ref=     1.4291    
 checkperc> Increasing con cutoff atoms   185  187 from     0.12892E-02 to     0.15741E-02 ref=     1.4045    
 checkperc> Increasing con cutoff atoms   185  188 from     0.36352E-02 to     0.37090E-02 ref=     2.1611    
 checkperc> Increasing con cutoff atoms   185  189 from     0.33788E-02 to     0.36728E-02 ref=     2.4306    
 checkperc> Increasing con cutoff atoms   185  191 from     0.43330E-02 to     0.51835E-02 ref=     2.8191    
 checkperc> Increasing con cutoff atoms   185  192 from     0.69119E-02 to     0.80857E-02 ref=     3.8971    
 checkperc> Increasing con cutoff atoms   185  193 from     0.57441E-02 to     0.58498E-02 ref=     2.4844    
 checkperc> Increasing con cutoff atoms   186  187 from     0.33038E-02 to     0.40968E-02 ref=     2.1664    
 checkperc> Increasing con cutoff atoms   186  188 from     0.85849E-02 to     0.89128E-02 ref=     2.5008    
 checkperc> Increasing con cutoff atoms   186  189 from     0.38934E-02 to     0.44027E-02 ref=     3.4153    
 checkperc> Increasing con cutoff atoms   186  190 from     0.47378E-02 to     0.50194E-02 ref=     4.3100    
 checkperc> Increasing con cutoff atoms   186  191 from     0.45334E-02 to     0.50687E-02 ref=     3.8997    
 checkperc> Increasing con cutoff atoms   186  192 from     0.71026E-02 to     0.79534E-02 ref=     4.9777    
 checkperc> Increasing con cutoff atoms   186  193 from     0.41539E-02 to     0.49328E-02 ref=     3.4572    
 checkperc> Increasing con cutoff atoms   187  189 from     0.82254E-03 to     0.10252E-02 ref=     1.4061    
 checkperc> Increasing con cutoff atoms   187  192 from     0.59976E-02 to     0.74565E-02 ref=     3.4143    
 checkperc> Increasing con cutoff atoms   187  193 from     0.78280E-02 to     0.81756E-02 ref=     2.8592    
 checkperc> Increasing con cutoff atoms   188  189 from     0.32498E-02 to     0.32800E-02 ref=     2.1610    
 checkperc> Increasing con cutoff atoms   188  192 from     0.58424E-02 to     0.68743E-02 ref=     4.3057    
 checkperc> Increasing con cutoff atoms   188  193 from     0.77496E-02 to     0.79364E-02 ref=     3.9411    
 checkperc> Increasing con cutoff atoms   189  192 from     0.68053E-02 to     0.81268E-02 ref=     2.1528    
 checkperc> Increasing con cutoff atoms   189  193 from     0.48914E-02 to     0.56522E-02 ref=     2.4611    
 checkperc> Increasing con cutoff atoms   190  192 from     0.11032E-01 to     0.12539E-01 ref=     2.4749    
 checkperc> Increasing con cutoff atoms   190  193 from     0.38256E-02 to     0.47242E-02 ref=     3.4333    
 checkperc> Increasing con cutoff atoms   191  192 from     0.28103E-02 to     0.31041E-02 ref=     1.0786    
 initialise> Interpolation metric value for minima 1 and 2 is      31.71326452    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     27091.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.00     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=    39
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    221 fraction=    0.990000 images=     3 time=       0.8
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    246 steps, energy/image=    -401.5479741     RMS=9.285934597     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   34.54     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0768 Dev= 4.04% S= 33.06 time= 26.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=  47.70

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1430 steps. Energy=    -446.0492388       time=      19.23
 Minus side of path:                    1813 steps. Energy=    -447.1095793       time=      25.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0492388 0.83682         -445.2124156  1.8972         -447.1095793  63.996  30.027   1.736 125.566
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -446.0492388 0.83682        -445.2124156  1.8972        -447.1095793  63.996  30.027   1.736 125.566

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

 Elapsed time=                               120.84
 OPTIM> # of energy calls=                          2 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=              8592 time=          64.62 %= 53.5
 OPTIM> # of energy+gradient+Hessian calls=        55 time=          15.92 %= 13.2
