
 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 05/23/2012 at 21:46:14
  [-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=    -446.9606864     RMS force=    0.8384037504E-06
 OPTIM> Final energy  =    -449.3696447     RMS force=    0.9137289059E-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=    0.22164E+06
 decide> The unconnected minima in the chain and their distances are:
     2       60.52     1 
 

 tryconnect> 630-iteration DNEB run for minima 1_S and 2_F using 18 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.1365657147    
 Double-ended search iterations= 630 RMS= 0.0339 Dev= 4.70% S= 72.57 time= 86.12
 Following    3 images are candidates for TS:    4    7   14  
 Converged to TS (number of iterations):        248
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         35
 DNEB run yielded 2 true transition state(s) time= 297.36

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1646 steps. Energy=    -446.9606864       time=      21.80
 Minus side of path:                    1578 steps. Energy=    -448.7791228       time=      18.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.9606864  1.7764         -445.1842794  3.5948         -448.7791228  85.032  77.846   1.936 112.623
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1342 steps. Energy=    -449.3696447       time=      14.76
 Minus side of path:                    1371 steps. Energy=    -450.2797410       time=      15.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3696447 0.31755         -449.0520914  1.2276         -450.2797410  26.413  25.418   5.851  37.256
        Known (#2)                                              *NEW* (Placed in 4)
 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=    0.10455E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.11     3 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 3_S using 14 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.3994903209    
 Double-ended search iterations= 490 RMS= 0.3531 Dev= 2.05% S= 55.21 time= 51.97
 Following    2 images are candidates for TS:    8   13  
 Converged to TS (number of iterations):        225
 Converged to TS (number of iterations):         43
 DNEB run yielded 2 true transition state(s) time= 158.87

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1583 steps. Energy=    -451.3459882       time=      18.66
 Minus side of path:                    1632 steps. Energy=    -450.2797410       time=      19.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.3459882  2.8210         -448.5250168  1.7547         -450.2797410  92.797  79.418   2.295  94.990
        *NEW* (Placed in 5)                                     Known (#4)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1283 steps. Energy=    -448.7791228       time=      13.96
 Minus side of path:                    1306 steps. Energy=    -450.2685203       time=      14.56

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7791228  1.4794         -447.2997260  2.9688         -450.2685203  25.483  24.492   5.033  43.317
        Known (#3)                                              *NEW* (Placed in 6)
 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=     34512.    
 decide> The unconnected minima in the chain and their distances are:
     5       32.56     6 
 

 tryconnect> 315-iteration DNEB run for minima 5_F and 6_S using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0603 Dev= 1.85% S= 34.94 time= 21.27
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  25.96

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1289 steps. Energy=    -449.6188951       time=      14.32
 Minus side of path:                    1307 steps. Energy=    -450.2685203       time=      14.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.6188951  2.7352         -446.8837288  3.3848         -450.2685203  12.095  10.053   5.503  39.616
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     16143.    
 decide> The unconnected minima in the chain and their distances are:
     5       25.27     7 
 

 tryconnect> 245-iteration DNEB run for minima 5_F and 7_S using 7 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0606 Dev= 0.29% S= 25.79 time= 12.88
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  42.18

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1389 steps. Energy=    -450.6547204       time=      15.24
 Minus side of path:                    1307 steps. Energy=    -451.3459882       time=      13.86

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6547204  1.0873         -449.5674440  1.7785         -451.3459882  32.310  27.176   2.183  99.879
        *NEW* (Placed in 8)                                     Known (#5)
 Unconnected minimum 8 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     76.255    
 decide> The unconnected minima in the chain and their distances are:
     8        4.24     7 
 

 tryconnect> 70-iteration DNEB run for minima 7_S and 8_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0571 Dev= 0.09% S= 4.32 time= 1.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  21.27

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1281 steps. Energy=    -449.6188951       time=      13.48
 Minus side of path:                    1286 steps. Energy=    -450.6547204       time=      13.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.6188951 0.61100E-01     -449.5577953  1.0969         -450.6547204   4.706   4.240  19.169  11.373
        Known (#7)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -446.9606864  1.7764        -445.1842794  3.5948        -448.7791228  85.032  77.846   1.936 112.623
   4     -448.7791228  1.4794        -447.2997260  2.9688        -450.2685203  25.483  24.492   5.033  43.317
   5     -450.2685203  3.3848        -446.8837288  2.7352        -449.6188951  12.095  10.053   5.503  39.616
   7     -449.6188951 0.61100E-01    -449.5577953  1.0969        -450.6547204   4.706   4.240  19.169  11.373
   6     -450.6547204  1.0873        -449.5674440  1.7785        -451.3459882  32.310  27.176   2.183  99.879
   3     -451.3459882  2.8210        -448.5250168  1.7547        -450.2797410  92.797  79.418   2.295  94.990
   2     -450.2797410  1.2276        -449.0520914 0.31755        -449.3696447  26.413  25.418   5.851  37.256

 Number of TS in the path       =      7
 Number of cycles               =      5

 Elapsed time=                               941.63
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             55881 time=         418.76 %= 44.5
 OPTIM> # of energy+gradient+Hessian calls=       916 time=         258.91 %= 27.5
