
 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 05/25/2012 at 12:50:07
  [-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> 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
 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> 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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> using simple internal interpolation.    Image points will not be evenly distributed in Cartesians
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -450.8498751     RMS force=    0.9777345081E-06
 OPTIM> Final energy  =    -450.4694291     RMS force=    0.9949809802E-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 is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.14084E+06
 decide> The unconnected minima in the chain and their distances are:
     2       52.03     1 
 

 tryconnect> 525-iteration DNEB run for minima 1_S and 2_F using 15 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 525 RMS= 0.2220 Dev= 6.52% S= 58.49 time= 60.54
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=  65.12

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1291 steps. Energy=    -449.2954746       time=      15.16
 Minus side of path:                    1355 steps. Energy=    -450.8498751       time=      16.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2954746 0.78060E-01     -449.2174150  1.6325         -450.8498751  22.637  22.131   1.783 122.272
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     49708.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.77     3 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 3_S using 11 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0643 Dev= 4.34% S= 41.23 time= 32.42
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):         30
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 147.57

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1304 steps. Energy=    -449.2354845       time=      13.65
 Minus side of path:                    1457 steps. Energy=    -450.4694291       time=      16.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2354845  3.8073         -445.4282179  5.0412         -450.4694291  32.545  30.626   2.101 103.751
        *NEW* (Placed in 4)                                     Known (#2)
 Unconnected minimum 4 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     12625.    
 decide> The unconnected minima in the chain and their distances are:
     4       23.28     3 
 

 tryconnect> 210-iteration DNEB run for minima 3_S and 4_F using 6 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1429 Dev= 0.72% S= 24.33 time= 9.59
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=  57.47

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1364 steps. Energy=    -449.2354845       time=      14.47
 Minus side of path:                    1761 steps. Energy=    -449.3135815       time=      21.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.2354845 0.28267         -448.9528168 0.36076         -449.3135815  37.935  29.913   1.901 114.671
        Known (#4)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2254.3    
 decide> The unconnected minima in the chain and their distances are:
     5       13.11     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 5_F using 3 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 105 RMS= 0.1625 Dev= 0.22% S= 14.06 time= 2.42
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=  26.90

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1292 steps. Energy=    -449.0871717       time=      13.40
 Minus side of path:                    1319 steps. Energy=    -450.8498751       time=      13.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0871717  3.4641         -445.6231145  5.2268         -450.8498751  13.321   8.909   6.786  32.124
        *NEW* (Placed in 6)                                     Known (#1)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     859.20    
 decide> The unconnected minima in the chain and their distances are:
     5        9.51     6 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 6_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0718 Dev= 0.03% S= 9.54 time= 1.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=  36.65

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1357 steps. Energy=    -449.0871717       time=      14.34
 Minus side of path:                    1450 steps. Energy=    -449.2354845       time=      15.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0871717 0.19401         -448.8931655 0.34232         -449.2354845  26.742  26.258   1.892 115.239
        Known (#6)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -450.8498751  5.2268        -445.6231145  3.4641        -449.0871717  13.321   8.909   6.786  32.124
   5     -449.0871717 0.19401        -448.8931655 0.34232        -449.2354845  26.742  26.258   1.892 115.239
   2     -449.2354845  3.8073        -445.4282179  5.0412        -450.4694291  32.545  30.626   2.101 103.751

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

 Elapsed time=                               594.97
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             36214 time=         271.61 %= 45.7
 OPTIM> # of energy+gradient+Hessian calls=       578 time=         164.49 %= 27.6
