
 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 22:09:24
  [-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=    -460.3176882     RMS force=    0.9578702121E-06
 OPTIM> Final energy  =    -461.8916769     RMS force=    0.9495079478E-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      12.42708610    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     1900.2    
 decide> The unconnected minima in the chain and their distances are:
     2       12.37     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=   171
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     64 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     89 steps, energy/image=    -452.2736425     RMS=.9073897389     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   13.24     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1780 Dev= 0.69% S= 12.93 time= 2.35
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=  28.63

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1176 steps. Energy=    -460.3176882       time=      13.02
 Minus side of path:                    1158 steps. Energy=    -462.4882394       time=      13.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -460.3176882  1.1691         -459.1485529  3.3397         -462.4882394  15.293  11.418   2.203  98.954
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms     1    3 from     0.31419E-02 to     0.31552E-02 ref=     1.0117    
 checkperc> Increasing con cutoff atoms    22   31 from     0.27278E-02 to     0.28964E-02 ref=     4.6359    
 checkperc> Increasing con cutoff atoms    22   32 from     0.44622E-02 to     0.45103E-02 ref=     5.6569    
 checkperc> Increasing con cutoff atoms    28   29 from     0.36371E-02 to     0.47856E-02 ref=     2.1643    
 checkperc> Increasing con cutoff atoms    28   30 from     0.69649E-02 to     0.83521E-02 ref=     2.4992    
 checkperc> Increasing con cutoff atoms    28   31 from     0.36607E-02 to     0.43571E-02 ref=     3.4147    
 checkperc> Increasing con cutoff atoms    28   32 from     0.36411E-02 to     0.54563E-02 ref=     4.3091    
 checkperc> Increasing con cutoff atoms    29   31 from     0.10700E-02 to     0.13303E-02 ref=     1.4058    
 checkperc> Increasing con cutoff atoms    50   55 from     0.13657     to     0.15216     ref=     2.7313    
 checkperc> Increasing con cutoff atoms    60   61 from     0.74675E-03 to     0.78765E-03 ref=     1.0839    
 checkperc> Increasing con cutoff atoms    72   73 from     0.46475E-02 to     0.49880E-02 ref=     2.1601    
 checkperc> Increasing con cutoff atoms    83   85 from     0.17285E-02 to     0.17895E-02 ref=     1.0902    
 checkperc> Increasing con cutoff atoms   111  113 from     0.77635E-02 to     0.81971E-02 ref=     3.1329    
 checkperc> Increasing con cutoff atoms   114  119 from     0.47840E-01 to     0.50237E-01 ref=     2.6004    
 checkperc> Increasing con cutoff atoms   118  119 from     0.33077E-01 to     0.33081E-01 ref=     2.1566    
 checkperc> Increasing con cutoff atoms   136  156 from     0.50893E-02 to     0.59216E-02 ref=     1.5445    
 checkperc> Increasing con cutoff atoms   158  159 from     0.31581E-02 to     0.32477E-02 ref=     1.0112    
 checkperc> Increasing con cutoff atoms   163  168 from     0.13375E-01 to     0.13453E-01 ref=     2.0539    
 checkperc> Increasing con cutoff atoms   172  176 from     0.27698E-01 to     0.30803E-01 ref=     2.4500    
 checkperc> Increasing con cutoff atoms   174  176 from     0.66696E-02 to     0.72103E-02 ref=     1.5376    
 checkperc> Increasing con cutoff atoms   174  177 from     0.14552E-01 to     0.15034E-01 ref=     2.1516    
 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=     345.60    
 decide> The unconnected minima in the chain and their distances are:
     2        7.01     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=   214
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -457.1284110     RMS=.8449523092E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   7.219     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2319 Dev= 0.57% S= 7.03 time= 1.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=  24.17

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1155 steps. Energy=    -462.4882394       time=      14.55
 Minus side of path:                    1168 steps. Energy=    -461.8916769       time=      13.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -462.4882394 0.93987         -461.5483648 0.34331         -461.8916769   7.735   7.011   2.082 104.689
        Known (#3)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -460.3176882  1.1691        -459.1485529  3.3397        -462.4882394  15.293  11.418   2.203  98.954
   2     -462.4882394 0.93987        -461.5483648 0.34331        -461.8916769   7.735   7.011   2.082 104.689

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

 Elapsed time=                               112.17
 OPTIM> # of energy calls=                          4 time=           0.03 %=  0.0
 OPTIM> # of energy+gradient calls=              7603 time=          56.86 %= 50.7
 OPTIM> # of energy+gradient+Hessian calls=        60 time=          17.60 %= 15.7
