
 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 22:16:44
  [-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=    -538.5809425     RMS force=    0.8058521419E-06
 OPTIM> Final energy  =    -532.4369020     RMS force=    0.9305464924E-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      64.03355913    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     48841.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.49     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=    22
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    445 fraction=    0.990000 images=     4 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    470 steps, energy/image=    -511.4126992     RMS=1.649349415     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   44.57     Attempts, images and iterations=     0    13   455
 lbfgs> Final DNEB force constant     0.1179705990    
 Double-ended search iterations= 455 RMS= 0.0563 Dev= 4.02% S= 51.10 time= 12.58
 Following    2 images are candidates for TS:    7   13  
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):         55
 DNEB run yielded 2 true transition state(s) time=  14.53

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     898 steps. Energy=    -531.2396179       time=       2.34
 Minus side of path:                     803 steps. Energy=    -538.5809425       time=       2.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.2396179 0.96804         -530.2715737  8.3094         -538.5809425  28.555  26.276   2.512  42.600
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    17   20 from     0.14608E-01 to     0.14788E-01 ref=     2.0128    
 checkperc> Increasing con cutoff atoms    56   57 from     0.20501E-01 to     0.21847E-01 ref=     2.1325    
 checkperc> Increasing con cutoff atoms    57   58 from     0.66525E-03 to     0.13147E-02 ref=     1.0922    
 checkperc> Increasing con cutoff atoms    71   72 from     0.15394E-01 to     0.19673E-01 ref=     2.2509    
 checkperc> Increasing con cutoff atoms    71   74 from     0.61561E-01 to     0.75984E-01 ref=     2.8619    
 checkperc> Increasing con cutoff atoms    72   76 from     0.36660E-01 to     0.41857E-01 ref=     2.4629    
 checkperc> Increasing con cutoff atoms    74   79 from     0.51030E-01 to     0.51788E-01 ref=     2.5880    
 checkperc> Increasing con cutoff atoms    94   96 from     0.14061E-02 to     0.14955E-02 ref=     1.4090    
 checkperc> Increasing con cutoff atoms    95   96 from     0.27586E-02 to     0.28880E-02 ref=     2.1633    
 checkperc> Increasing con cutoff atoms    99  101 from     0.10339E-01 to     0.10739E-01 ref=     2.4042    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     701 steps. Energy=    -533.9330584       time=       1.73
 Minus side of path:                     681 steps. Energy=    -534.2125231       time=       1.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.9330584 0.57593         -533.3571322 0.85539         -534.2125231  13.730   9.708   6.681  16.015
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    19   21 from     0.41664E-02 to     0.41705E-02 ref=     1.0134    
 checkperc> Increasing con cutoff atoms    39   41 from     0.78866E-01 to     0.79046E-01 ref=     2.9344    
 checkperc> Increasing con cutoff atoms    72   75 from     0.21879E-01 to     0.22132E-01 ref=     2.0800    
 checkperc> Increasing con cutoff atoms    17   20 from     0.14788E-01 to     0.14796E-01 ref=     2.0128    
 checkperc> Increasing con cutoff atoms    37   38 from     0.96347E-02 to     0.10318E-01 ref=     2.2418    
 checkperc> Increasing con cutoff atoms    37   39 from     0.93999E-02 to     0.10383E-01 ref=     3.1323    
 checkperc> Increasing con cutoff atoms    56   57 from     0.21847E-01 to     0.22065E-01 ref=     2.1325    
 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=     2086.7    
 decide> The unconnected minima in the chain and their distances are:
     2        5.29     4     5       12.45     3 
 

 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=   103
 intlbfgs> Freezing     92 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     51 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     76 steps, energy/image=    -516.7974685     RMS=16.64063741     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      2     4 dist=   14.56     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 140 RMS= 0.5618 Dev= 0.59% S= 6.30 time= 1.14
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.52

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     630 steps. Energy=    -532.4369020       time=       1.57
 Minus side of path:                     658 steps. Energy=    -533.9330584       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.4369020 0.61485E-01     -532.3754170  1.5576         -533.9330584   6.494   5.297  30.271   3.535
        Known (#2)                                              Known (#4)
 Unconnected minimum 4 found its way to F set.

 tryconnect> Interpolation for minima 3_S and 5_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=    85
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     48 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     73 steps, energy/image=    -496.7728844     RMS=9.914184760     images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      3     5 dist=   19.52     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.4558 Dev= 1.55% S= 13.37 time= 1.78
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.39

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     697 steps. Energy=    -531.8692819       time=       1.72
 Minus side of path:                     643 steps. Energy=    -531.2396179       time=       1.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8692819 0.88185         -530.9874294 0.25219         -531.2396179   7.607   5.601  22.226   4.814
        *NEW* (Placed in 6)                                     Known (#3)
 checkperc> Increasing con cutoff atoms    17   20 from     0.14796E-01 to     0.14817E-01 ref=     2.0128    
 checkperc> Increasing con cutoff atoms    56   57 from     0.22065E-01 to     0.22677E-01 ref=     2.1325    
 checkperc> Increasing con cutoff atoms    72   75 from     0.22132E-01 to     0.25049E-01 ref=     2.0800    
 checkperc> Increasing con cutoff atoms    72   76 from     0.41857E-01 to     0.43754E-01 ref=     2.4629    
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1639.2    
 decide> The unconnected minima in the chain and their distances are:
     5       11.78     6 
 

 tryconnect> Interpolation for minima 5_F and 6_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=    88
 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=    -525.7023626     RMS=.7313489015     images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      5     6 dist=   17.91     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.0759 Dev= 1.54% S= 12.11 time= 1.77
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   4.77

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     733 steps. Energy=    -534.2125231       time=       1.82
 Minus side of path:                     634 steps. Energy=    -531.8692819       time=       1.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.2125231  2.3592         -531.8533678 0.15914E-01     -531.8692819  12.836  11.802   6.002  17.828
        Known (#5)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -538.5809425  8.3094        -530.2715737 0.96804        -531.2396179  28.555  26.276   2.512  42.600
   4     -531.2396179 0.25219        -530.9874294 0.88185        -531.8692819   7.607   5.601  22.226   4.814
   5     -531.8692819 0.15914E-01    -531.8533678  2.3592        -534.2125231  12.836  11.802   6.002  17.828
   2     -534.2125231 0.85539        -533.3571322 0.57593        -533.9330584  13.730   9.708   6.681  16.015
   3     -533.9330584  1.5576        -532.3754170 0.61485E-01    -532.4369020   6.494   5.297  30.271   3.535

 Number of TS in the path       =      5
 Number of cycles               =      3

 Elapsed time=                                63.05
 OPTIM> # of energy calls=                          8 time=           0.02 %=  0.0
 OPTIM> # of energy+gradient calls=             19207 time=          38.66 %= 61.3
 OPTIM> # of energy+gradient+Hessian calls=       209 time=          12.13 %= 19.2
