
 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 17:43:20
  [-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:         0.05000       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=    -456.3232521     RMS force=    0.9228759325E-06
 OPTIM> Final energy  =    -453.4164964     RMS force=    0.8854358076E-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      37.84455897    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     51996.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.29     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=    37
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    256 fraction=    0.990000 images=     3 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    281 steps, energy/image=    -440.2515122     RMS=.9917478486     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   39.88     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0314 Dev= 1.26% S= 40.98 time= 31.44
 Following    2 images are candidates for TS:    6    8  
 Converged to TS (number of iterations):        211
 Converged to TS (number of iterations):        108
 DNEB run yielded 2 true transition state(s) time= 161.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1208 steps. Energy=    -455.5998591       time=      12.22
 Minus side of path:                    1245 steps. Energy=    -455.5882836       time=      12.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5998591 0.33831         -455.2615489 0.32673         -455.5882836   6.907   6.369   3.236  67.368
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    26   29 from     0.16025E-02 to     0.16271E-02 ref=     2.4225    
 checkperc> Increasing con cutoff atoms    26   30 from     0.22043E-02 to     0.22413E-02 ref=     3.4062    
 checkperc> Increasing con cutoff atoms    27   29 from     0.46627E-03 to     0.61723E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    27   30 from     0.12366E-02 to     0.16964E-02 ref=     2.1615    
 checkperc> Increasing con cutoff atoms    50   53 from     0.10687E-01 to     0.11024E-01 ref=     2.0100    
 checkperc> Increasing con cutoff atoms    66   69 from     0.21468E-02 to     0.21723E-02 ref=     3.4151    
 checkperc> Increasing con cutoff atoms    80   89 from     0.36699E-01 to     0.37442E-01 ref=     2.5348    
 checkperc> Increasing con cutoff atoms    89   91 from     0.20146E-02 to     0.20256E-02 ref=     1.3380    
 checkperc> Increasing con cutoff atoms    89   94 from     0.93802E-01 to     0.11508     ref=     2.7004    
 checkperc> Increasing con cutoff atoms    92   94 from     0.88094E-01 to     0.91980E-01 ref=     2.8610    
 checkperc> Increasing con cutoff atoms    93  105 from     0.21551E-01 to     0.24101E-01 ref=     2.4736    
 checkperc> Increasing con cutoff atoms    93  106 from     0.35691E-01 to     0.40471E-01 ref=     2.5684    
 checkperc> Increasing con cutoff atoms   133  136 from     0.38236E-01 to     0.39093E-01 ref=     2.8592    
 checkperc> Increasing con cutoff atoms   151  153 from     0.93834E-03 to     0.12652E-02 ref=     1.4083    
 checkperc> Increasing con cutoff atoms   206  207 from     0.24998E-02 to     0.25325E-02 ref=     1.0894    
 checkperc> Increasing con cutoff atoms   206  215 from     0.66317E-01 to     0.99704E-01 ref=     2.7299    
 checkperc> Increasing con cutoff atoms   210  211 from     0.61299E-02 to     0.64561E-02 ref=     1.7660    
 checkperc> Increasing con cutoff atoms   210  214 from     0.51179E-01 to     0.68225E-01 ref=     2.4089    
 checkperc> Increasing con cutoff atoms   210  215 from     0.74703E-01 to     0.90204E-01 ref=     2.4602    
 checkperc> Increasing con cutoff atoms   211  213 from     0.72584E-01 to     0.88992E-01 ref=     2.4505    
 checkperc> Increasing con cutoff atoms   211  214 from     0.54002E-01 to     0.74021E-01 ref=     2.4559    
 checkperc> Increasing con cutoff atoms    26   29 from     0.16271E-02 to     0.16431E-02 ref=     2.4225    
 checkperc> Increasing con cutoff atoms    26   30 from     0.22413E-02 to     0.23235E-02 ref=     3.4062    
 checkperc> Increasing con cutoff atoms    27   29 from     0.61723E-03 to     0.71724E-03 ref=     1.4050    
 checkperc> Increasing con cutoff atoms    27   30 from     0.16964E-02 to     0.19393E-02 ref=     2.1615    
 checkperc> Increasing con cutoff atoms    79   89 from     0.14223E-01 to     0.14851E-01 ref=     2.1386    
 checkperc> Increasing con cutoff atoms    80   89 from     0.37442E-01 to     0.39158E-01 ref=     2.5348    
 checkperc> Increasing con cutoff atoms   114  134 from     0.23848E-01 to     0.27616E-01 ref=     2.4635    
 checkperc> Increasing con cutoff atoms   114  135 from     0.50951E-01 to     0.53740E-01 ref=     2.5562    
 checkperc> Increasing con cutoff atoms   118  119 from     0.23786E-01 to     0.24810E-01 ref=     2.1497    
 checkperc> Increasing con cutoff atoms   122  129 from     0.10961     to     0.11851     ref=     2.8077    
 checkperc> Increasing con cutoff atoms   126  130 from     0.77287E-01 to     0.88238E-01 ref=     2.3974    
 checkperc> Increasing con cutoff atoms   126  131 from     0.96992E-01 to     0.97741E-01 ref=     2.4705    
 checkperc> Increasing con cutoff atoms   127  129 from     0.91886E-01 to     0.96317E-01 ref=     2.4186    
 checkperc> Increasing con cutoff atoms   133  136 from     0.39093E-01 to     0.40173E-01 ref=     2.8592    
 checkperc> Increasing con cutoff atoms   203  209 from     0.45794E-01 to     0.47024E-01 ref=     2.5575    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1333 steps. Energy=    -455.5998591       time=      13.95
 Minus side of path:                    1212 steps. Energy=    -455.0287733       time=      12.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5998591  1.9717         -453.6282052  1.4006         -455.0287733  28.422  22.319   8.477  25.717
        Known (#3)                                              *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    26   27 from     0.70775E-03 to     0.84852E-03 ref=     1.4034    
 checkperc> Increasing con cutoff atoms    36   37 from     0.14982E-02 to     0.15584E-02 ref=     1.2356    
 checkperc> Increasing con cutoff atoms    77   78 from     0.12947E-01 to     0.14297E-01 ref=     2.1308    
 checkperc> Increasing con cutoff atoms   112  116 from     0.34272E-01 to     0.34575E-01 ref=     2.4484    
 checkperc> Increasing con cutoff atoms   113  115 from     0.70851E-01 to     0.70854E-01 ref=     2.9332    
 checkperc> Increasing con cutoff atoms   116  117 from     0.18630E-02 to     0.18671E-02 ref=     1.0908    
 checkperc> Increasing con cutoff atoms   210  212 from     0.11101E-01 to     0.11126E-01 ref=     2.1293    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     19843.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.99     5     4       13.07     1 
 

 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=   127
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     92 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    117 steps, energy/image=    -413.8895367     RMS=9.647134197     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   30.19     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0165 Dev= 0.73% S= 27.07 time= 21.03
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=  20.31

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1240 steps. Energy=    -453.4164964       time=      12.63
 Minus side of path:                    1311 steps. Energy=    -455.0287733       time=      13.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.4164964 0.17904         -453.2374556  1.7913         -455.0287733  26.786  25.995   4.885  44.624
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_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=   163
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     56 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     81 steps, energy/image=    -451.0058703     RMS=.2114717900     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   18.16     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 175 RMS= 2.2548 Dev= 1.39% S= 13.11 time= 6.52
 Following    1 images are candidates for TS:    4  
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=  23.05

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1234 steps. Energy=    -455.5882836       time=      12.59
 Minus side of path:                    1260 steps. Energy=    -456.3232520       time=      12.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5882836 0.48451E-01     -455.5398322 0.78342         -456.3232520  13.233  13.069   2.187  99.689
        Known (#4)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -456.3232521 0.78342        -455.5398322 0.48451E-01    -455.5882836  13.233  13.069   2.187  99.689
   1     -455.5882836 0.32673        -455.2615489 0.33831        -455.5998591   6.907   6.369   3.236  67.368
   2     -455.5998591  1.9717        -453.6282052  1.4006        -455.0287733  28.422  22.319   8.477  25.717
   3     -455.0287733  1.7913        -453.2374556 0.17904        -453.4164964  26.786  25.995   4.885  44.624

 Number of TS in the path       =      4
 Number of cycles               =      2

 Elapsed time=                               370.74
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             23739 time=         175.01 %= 47.2
 OPTIM> # of energy+gradient+Hessian calls=       366 time=         100.27 %= 27.0
