
 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 22:09:53
  [-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=    -448.5679478     RMS force=    0.9381255057E-06
 OPTIM> Final energy  =    -451.6762196     RMS force=    0.9517988604E-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      351.9162161    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.44968E+06
 decide> The unconnected minima in the chain and their distances are:
     2       76.26     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=     7
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1937 fraction=    0.990000 images=    11 time=       4.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1962 steps, energy/image=     2639.219444     RMS=18.46491529     images=  12
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   100.7     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.2245626974E-01
 Double-ended search iterations= 805 RMS= 0.0190 Dev= 6.74% S= 128.99 time= 140.73
 Following    2 images are candidates for TS:    8   14  
 Converged to TS (number of iterations):        153
 Converged to TS (number of iterations):        130
 DNEB run yielded 2 true transition state(s) time= 160.81

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    2111 steps. Energy=    -449.7567591       time=      32.22
 Minus side of path:                    1473 steps. Energy=    -448.1952917       time=      20.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7567591  3.0291         -446.7276528  1.4676         -448.1952917  89.148  70.903   4.280  50.934
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   119  123 from     0.18528E-01 to     0.18565E-01 ref=     2.1602    
 checkperc> Increasing con cutoff atoms   209  213 from     0.63975E-02 to     0.68591E-02 ref=     2.0793    
 checkperc> Increasing con cutoff atoms   160  161 from     0.84269E-03 to     0.92329E-03 ref=     1.0905    
 checkperc> Increasing con cutoff atoms   200  202 from     0.92003E-03 to     0.92351E-03 ref=     1.0908    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1309 steps. Energy=    -449.9061456       time=      14.95
 Minus side of path:                    1317 steps. Energy=    -449.7815669       time=      15.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9061456 0.21083         -449.6953177 0.86249E-01     -449.7815669  16.768  16.591   3.653  59.673
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 checkperc> Increasing con cutoff atoms   200  202 from     0.92351E-03 to     0.10583E-02 ref=     1.0908    
 checkperc> Increasing con cutoff atoms   200  204 from     0.20922E-01 to     0.23482E-01 ref=     2.1492    
 checkperc> Increasing con cutoff atoms   119  123 from     0.18565E-01 to     0.18746E-01 ref=     2.1602    
 checkperc> Increasing con cutoff atoms   200  204 from     0.23482E-01 to     0.23894E-01 ref=     2.1492    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 6 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=    0.12237E+06
 decide> The unconnected minima in the chain and their distances are:
     2       49.58     3     4        4.62     1 
 

 tryconnect> Interpolation for minima 2_F 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=    18
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    393 fraction=    0.990000 images=     5 time=       1.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    418 steps, energy/image=    -42.93573380     RMS=29.59041383     images=   5
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   56.28     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.4234464577E-01
 Double-ended search iterations= 560 RMS= 0.0270 Dev= 2.88% S= 53.29 time= 67.23
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  28.71

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1426 steps. Energy=    -450.6843206       time=      17.40
 Minus side of path:                    1521 steps. Energy=    -451.6762196       time=      17.70

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6843206 0.57398         -450.1103415  1.5659         -451.6762196  51.741  49.579   2.126 102.554
        *NEW* (Placed in 7)                                     Known (#2)
 checkperc> Increasing con cutoff atoms   209  213 from     0.68591E-02 to     0.69475E-02 ref=     2.0793    
 Unconnected minimum 7 found its way to F set.

 tryconnect> Interpolation for minima 1_S 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=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     19 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     44 steps, energy/image=    -444.0324585     RMS=.1128105324     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   5.072     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.1382 Dev= 0.46% S= 4.69 time= 1.05
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  20.76

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1331 steps. Energy=    -448.1952917       time=      15.42
 Minus side of path:                    1330 steps. Energy=    -448.5679478       time=      14.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.1952917 0.53222         -447.6630724 0.90488         -448.5679478   4.761   4.622   4.687  46.515
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2.0105    
 decide> The unconnected minima in the chain and their distances are:
     7        1.26     3 
 

 tryconnect> Interpolation for minima 3_S and 7_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=   217
 intlbfgs> Freezing    203 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     18 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     43 steps, energy/image=    -445.2532584     RMS=.2505377767E-01 images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   1.569     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0875 Dev= 1.69% S= 1.35 time= 1.06
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=  20.69

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1220 steps. Energy=    -449.7567591       time=      13.08
 Minus side of path:                    1249 steps. Energy=    -450.6843206       time=      13.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.7567591 0.11262         -449.6441425  1.0402         -450.6843206   1.363   1.261 165.935   1.314
        Known (#3)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -448.5679478 0.90488        -447.6630724 0.53222        -448.1952917   4.761   4.622   4.687  46.515
   1     -448.1952917  1.4676        -446.7276528  3.0291        -449.7567591  89.148  70.903   4.280  50.934
   5     -449.7567591 0.11262        -449.6441425  1.0402        -450.6843206   1.363   1.261 165.935   1.314
   3     -450.6843206 0.57398        -450.1103415  1.5659        -451.6762196  51.741  49.579   2.126 102.554

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                               627.39
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             49626 time=         370.08 %= 59.0
 OPTIM> # of energy+gradient+Hessian calls=       351 time=         102.95 %= 16.4
