
 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 22:12:20
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 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=    17
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>  321 Cartesian coordinates will be optimised for  107 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=    -530.4519442     RMS force=    0.9960492138E-06
 OPTIM> Final energy  =    -530.9975087     RMS force=    0.9549412177E-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      77.61373003    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     11472.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.48     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=    63
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> Backtracking      1 steps, current active atoms=    70
 intlbfgs> switch on true potential at step    974 fraction=    0.990000 images=     4 time=       0.4
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    999 steps, energy/image=    -508.7355846     RMS=1.016643073     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   38.69     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant      1.112965089    
 Double-ended search iterations= 385 RMS= 0.1066 Dev= 1.37% S= 32.06 time= 8.70
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   6.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     782 steps. Energy=    -529.8728231       time=       2.07
 Minus side of path:                     678 steps. Energy=    -529.3520802       time=       1.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8728231  2.9705         -526.9022862  2.4498         -529.3520802  22.396  14.731   5.664  18.892
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    17   21 from     0.70920E-02 to     0.76863E-02 ref=     2.0304    
 checkperc> Increasing con cutoff atoms    34   35 from     0.64999E-02 to     0.81385E-02 ref=     1.7593    
 checkperc> Increasing con cutoff atoms    88   98 from     0.59824E-01 to     0.60057E-01 ref=     5.2060    
 checkperc> Increasing con cutoff atoms    93   96 from     0.45194E-02 to     0.47837E-02 ref=     2.4426    
 checkperc> Increasing con cutoff atoms    93  102 from     0.49904E-02 to     0.55737E-02 ref=     3.4216    
 checkperc> Increasing con cutoff atoms    95  104 from     0.65424E-02 to     0.65810E-02 ref=     4.3119    
 checkperc> Increasing con cutoff atoms    98  104 from     0.39687E-02 to     0.45808E-02 ref=     3.4234    
 checkperc> Increasing con cutoff atoms    99  104 from     0.11623E-01 to     0.12372E-01 ref=     4.5631    
 checkperc> Increasing con cutoff atoms   101  104 from     0.46543E-02 to     0.51840E-02 ref=     2.1614    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     830.88    
 decide> The unconnected minima in the chain and their distances are:
     2        7.56     4     3        7.35     1 
 

 tryconnect> Interpolation for minima 2_F and 4_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=    95
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     24 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     49 steps, energy/image=    -513.7710260     RMS=12.28095311     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   14.40     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 140 RMS= 1.0006 Dev= 0.91% S= 8.30 time= 1.15
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         75
 DNEB run yielded 1 true transition state(s) time=   7.49

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     741 steps. Energy=    -532.3570695       time=       1.94
 Minus side of path:                     608 steps. Energy=    -530.9975087       time=       1.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3570695  3.2939         -529.0631341  1.9344         -530.9975087  22.646  20.721   2.418  44.250
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 3_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=    89
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     20 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     45 steps, energy/image=    -515.2763688     RMS=10.18705195     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   14.65     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 140 RMS= 0.0394 Dev= 0.66% S= 7.39 time= 1.15
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         16
 DNEB run yielded 1 true transition state(s) time=   2.65

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     586 steps. Energy=    -529.8728231       time=       1.45
 Minus side of path:                     600 steps. Energy=    -530.4519442       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.8728231 0.24392E-01     -529.8484309 0.60351         -530.4519442   7.591   7.346   3.511  30.479
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 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=     866.47    
 decide> The unconnected minima in the chain and their distances are:
     2        7.56     4 
 

 tryconnect> Interpolation for minima 2_F and 4_S using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    95
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     25 fraction=    0.990000 images=    15 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     50 steps, energy/image=    -521.6573829     RMS=2.296838207     images=  15
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   11.58     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant      17.10339358    
 Double-ended search iterations= 805 RMS= 1.8173 Dev= 3.93% S= 12.50 time= 38.78
 Following    3 images are candidates for TS:    8   13   21  
 Converged to TS (number of iterations):         12
 Converged to TS (number of iterations):         12
 Converged to TS (number of iterations):         26
 DNEB run yielded 3 true transition state(s) time=   9.57
 isnewts> transition state is the same as number        4 energy=     -522.2427844647
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     651 steps. Energy=    -529.4054500       time=       1.61
 Minus side of path:                     596 steps. Energy=    -530.9975087       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.4054500  7.1627         -522.2427845  8.7547         -530.9975087   8.463   7.690   9.385  11.401
        *NEW* (Placed in 6)                                     Known (#2)
 checkperc> Increasing con cutoff atoms    17   21 from     0.76863E-02 to     0.83200E-02 ref=     2.0304    
 checkperc> Increasing con cutoff atoms    34   35 from     0.81385E-02 to     0.83268E-02 ref=     1.7593    
 checkperc> Increasing con cutoff atoms    58   70 from     0.26507E-01 to     0.28070E-01 ref=     2.1363    
 checkperc> Increasing con cutoff atoms    60   63 from     0.16439E-01 to     0.16731E-01 ref=     3.0449    
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     645 steps. Energy=    -529.4054500       time=       1.61
 Minus side of path:                     589 steps. Energy=    -530.9975087       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.4054500  7.1627         -522.2427845  8.7547         -530.9975087   8.464   7.691   9.344  11.452
        Known (#6)                                              Known (#2)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     777 steps. Energy=    -531.8541018       time=       1.98
 Minus side of path:                     630 steps. Energy=    -532.3570695       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8541018  8.4132         -523.4409050  8.9162         -532.3570695   9.529   4.044  21.971   4.870
        *NEW* (Placed in 7)                                     Known (#5)
 checkperc> Increasing con cutoff atoms    88   92 from     0.14437E-01 to     0.14851E-01 ref=     2.1579    
 checkperc> Increasing con cutoff atoms    95   96 from     0.27586E-02 to     0.30097E-02 ref=     2.1633    
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.53606    
 decide> The unconnected minima in the chain and their distances are:
     6        0.81     4 
 

 tryconnect> Interpolation for minima 4_S and 6_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=   107
 intlbfgs> Freezing     92 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=    -524.0461259     RMS=.5357395433E-01 images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      4     6 dist=   1.575     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      10.00000000    
 Double-ended search iterations= 70 RMS= 0.0147 Dev= 0.88% S= 0.81 time= 0.29
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.14

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     576 steps. Energy=    -529.3520802       time=       1.38
 Minus side of path:                     599 steps. Energy=    -529.4054500       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.3520802 0.99334E-03     -529.3510869 0.54363E-01     -529.4054500   0.813   0.812   6.387  16.753
        Known (#4)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -530.4519442 0.60351        -529.8484309 0.24392E-01    -529.8728231   7.591   7.346   3.511  30.479
   1     -529.8728231  2.9705        -526.9022862  2.4498        -529.3520802  22.396  14.731   5.664  18.892
   7     -529.3520802 0.99334E-03    -529.3510869 0.54363E-01    -529.4054500   0.813   0.812   6.387  16.753
   4     -529.4054500  7.1627        -522.2427845  8.7547        -530.9975087   8.463   7.690   9.385  11.401

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

 Elapsed time=                               103.95
 OPTIM> # of energy calls=                         10 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             38533 time=          77.75 %= 74.8
 OPTIM> # of energy+gradient+Hessian calls=       206 time=          11.62 %= 11.2
