
 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 22:10:31
  [-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=    -451.5683682     RMS force=    0.8376113907E-06
 OPTIM> Final energy  =    -453.7136852     RMS force=    0.9192813669E-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      58.98404133    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.17579E+06
 decide> The unconnected minima in the chain and their distances are:
     2       55.96     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=    14
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    534 fraction=    0.990000 images=     6 time=       1.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    559 steps, energy/image=    -426.9613908     RMS=.6908740173     images=   7
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   60.68     Attempts, images and iterations=     0    18   630
 lbfgs> Final DNEB force constant     0.4404380788    
 Double-ended search iterations= 630 RMS= 0.0390 Dev= 3.75% S= 63.19 time= 84.47
 Following    2 images are candidates for TS:   11   14  
 Converged to TS (number of iterations):         55
 Converged to TS (number of iterations):        199
 DNEB run yielded 2 true transition state(s) time= 158.86

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1461 steps. Energy=    -451.5683682       time=      16.78
 Minus side of path:                    1410 steps. Energy=    -450.3794731       time=      15.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5683682  1.8054         -449.7629547 0.61652         -450.3794731  49.274  47.740   2.333  93.439
        Known (#1)                                              *NEW* (Placed in 3)
 checkperc> Increasing con cutoff atoms     1    7 from     0.46676E-02 to     0.46692E-02 ref=     2.4898    
 checkperc> Increasing con cutoff atoms     2    7 from     0.32706E-01 to     0.32719E-01 ref=     2.6309    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1275 steps. Energy=    -453.7136852       time=      13.92
 Minus side of path:                    1231 steps. Energy=    -453.5148884       time=      13.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7136852 0.35296         -453.3607228 0.15417         -453.5148884  26.904  26.562   3.333  65.407
        Known (#2)                                              *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms     1    9 from     0.30658E-02 to     0.30695E-02 ref=     3.4278    
 checkperc> Increasing con cutoff atoms     3    7 from     0.35951E-02 to     0.36003E-02 ref=     3.3710    
 checkperc> Increasing con cutoff atoms    40   54 from     0.22641E-01 to     0.22648E-01 ref=     3.8532    
 checkperc> Increasing con cutoff atoms   103  104 from     0.23150E-02 to     0.24130E-02 ref=     1.2349    
 checkperc> Increasing con cutoff atoms   132  136 from     0.21287E-01 to     0.25996E-01 ref=     2.4966    
 checkperc> Increasing con cutoff atoms   133  136 from     0.48096E-01 to     0.50995E-01 ref=     2.8594    
 checkperc> Increasing con cutoff atoms   160  164 from     0.25419E-01 to     0.25490E-01 ref=     2.5491    
 checkperc> Increasing con cutoff atoms   160  167 from     0.16098E-01 to     0.16645E-01 ref=     3.4867    
 checkperc> Increasing con cutoff atoms   160  174 from     0.29922E-01 to     0.33017E-01 ref=     3.8519    
 checkperc> Increasing con cutoff atoms   176  179 from     0.56944E-02 to     0.60885E-02 ref=     1.5025    
 checkperc> Increasing con cutoff atoms   176  184 from     0.16957E-01 to     0.17292E-01 ref=     3.8213    
 checkperc> Increasing con cutoff atoms   176  185 from     0.25890E-01 to     0.26091E-01 ref=     5.1140    
 checkperc> Increasing con cutoff atoms   176  186 from     0.16856E-01 to     0.17444E-01 ref=     5.9810    
 checkperc> Increasing con cutoff atoms   179  184 from     0.41171E-02 to     0.41380E-02 ref=     2.3488    
 checkperc> Increasing con cutoff atoms   179  185 from     0.61418E-02 to     0.65127E-02 ref=     3.6935    
 checkperc> Increasing con cutoff atoms   179  187 from     0.11037E-01 to     0.12095E-01 ref=     4.2991    
 checkperc> Increasing con cutoff atoms   179  188 from     0.10217E-01 to     0.11303E-01 ref=     5.3789    
 checkperc> Increasing con cutoff atoms   179  189 from     0.12426E-01 to     0.13265E-01 ref=     3.8952    
 checkperc> Increasing con cutoff atoms   179  190 from     0.11944E-01 to     0.12036E-01 ref=     4.8056    
 checkperc> Increasing con cutoff atoms   179  191 from     0.12479E-01 to     0.13088E-01 ref=     2.6639    
 checkperc> Increasing con cutoff atoms   179  193 from     0.54438E-02 to     0.57342E-02 ref=     1.4675    
 checkperc> Increasing con cutoff atoms   184  192 from     0.53298E-02 to     0.55207E-02 ref=     3.4033    
 checkperc> Increasing con cutoff atoms   185  193 from     0.49424E-02 to     0.50181E-02 ref=     2.4852    
 checkperc> Increasing con cutoff atoms   186  193 from     0.36211E-02 to     0.36884E-02 ref=     3.4584    
 checkperc> Increasing con cutoff atoms   187  193 from     0.74984E-02 to     0.78875E-02 ref=     2.8598    
 checkperc> Increasing con cutoff atoms   188  193 from     0.70615E-02 to     0.73637E-02 ref=     3.9420    
 checkperc> Increasing con cutoff atoms   189  193 from     0.49989E-02 to     0.52069E-02 ref=     2.4616    
 checkperc> Increasing con cutoff atoms   191  192 from     0.28892E-02 to     0.29882E-02 ref=     1.0784    
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     16746.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.56     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=    58
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    206 fraction=    0.990000 images=     3 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    231 steps, energy/image=    -444.9740990     RMS=.5729740178     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   27.08     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0692 Dev= 1.22% S= 27.03 time= 16.79
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         77
 DNEB run yielded 1 true transition state(s) time=  54.68

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1241 steps. Energy=    -450.3794731       time=      14.73
 Minus side of path:                    1396 steps. Energy=    -453.0994666       time=      15.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.3794731 0.47899E-02     -450.3746831  2.7248         -453.0994666  22.777  22.651   1.645 132.512
        Known (#3)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     912.59    
 decide> The unconnected minima in the chain and their distances are:
     2        9.69     5 
 

 tryconnect> Interpolation for minima 2_F and 5_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=   203
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     45 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     70 steps, energy/image=    -446.5214392     RMS=.3670278656     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      2     5 dist=   11.68     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.2310 Dev= 1.10% S= 10.22 time= 2.37
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  22.23

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1297 steps. Energy=    -453.7136852       time=      14.64
 Minus side of path:                    1267 steps. Energy=    -453.0994666       time=      14.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7136852  3.1556         -450.5580665  2.5414         -453.0994666  10.802   9.694   4.889  44.594
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -451.5683682  1.8054        -449.7629547 0.61652        -450.3794731  49.274  47.740   2.333  93.439
   3     -450.3794731 0.47900E-02    -450.3746831  2.7248        -453.0994666  22.777  22.651   1.645 132.512
   4     -453.0994666  2.5414        -450.5580665  3.1556        -453.7136852  10.802   9.694   4.889  44.594

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

 Elapsed time=                               463.67
 OPTIM> # of energy calls=                          6 time=           0.04 %=  0.0
 OPTIM> # of energy+gradient calls=             30958 time=         229.53 %= 49.5
 OPTIM> # of energy+gradient+Hessian calls=       350 time=         106.31 %= 22.9
