
 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 05/24/2012 at 11:06:44
  [-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> 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
 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -529.6554571     RMS force=    0.9668610016E-06
 OPTIM> Final energy  =    -539.6623457     RMS force=    0.8397805913E-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=     73573.    
 decide> The unconnected minima in the chain and their distances are:
     2       41.90     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 2_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3623494974    
 Double-ended search iterations= 420 RMS= 0.0946 Dev= 2.49% S= 51.08 time= 10.11
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         19
 Converged to TS (number of iterations):         39
 DNEB run yielded 2 true transition state(s) time=   7.38

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     594 steps. Energy=    -529.6554571       time=       1.45
 Minus side of path:                     636 steps. Energy=    -530.8886546       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -529.6554571 0.44458         -529.2108807  1.6778         -530.8886546   5.846   5.374  11.395   9.390
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     693 steps. Energy=    -532.3308917       time=       1.74
 Minus side of path:                     835 steps. Energy=    -530.8886546       time=       2.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3308917  3.7500         -528.5808433  2.3078         -530.8886546  23.541   8.260   2.876  37.209
        *NEW* (Placed in 4)                                     Known (#3)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     59521.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.04     4 
 

 tryconnect> 385-iteration DNEB run for minima 2_F and 4_S using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 385 RMS= 0.2313 Dev= 1.75% S= 45.70 time= 8.50
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.79

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     644 steps. Energy=    -530.6427935       time=       1.64
 Minus side of path:                     604 steps. Energy=    -528.9930536       time=       1.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.6427935  1.7859         -528.8569192 0.13613         -528.9930536   8.369   7.876   2.249  47.569
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     15079.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.21     6     5       16.04     4 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.3304 Dev= 0.53% S= 23.18 time= 2.54
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=   3.27

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     772 steps. Energy=    -537.4922044       time=       2.00
 Minus side of path:                     626 steps. Energy=    -528.9930536       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.4922044  8.5447         -528.9475006 0.45553E-01     -528.9930536  20.085  19.806   1.819  58.824
        *NEW* (Placed in 7)                                     Known (#6)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 4_S and 5_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1557 Dev= 0.26% S= 16.77 time= 1.15
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=   5.66

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     626 steps. Energy=    -530.7625126       time=       1.62
 Minus side of path:                     620 steps. Energy=    -532.3308917       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7625126 0.52235         -530.2401628  2.0907         -532.3308917  15.815  12.040   5.909  18.108
        *NEW* (Placed in 8)                                     Known (#4)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      2 missing connections, weight=     1532.2    
 decide> The unconnected minima in the chain and their distances are:
     2       10.20     7     5        7.79     8 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.2664 Dev= 0.12% S= 10.65 time= 0.64
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   3.99

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     571 steps. Energy=    -538.7028350       time=       1.41
 Minus side of path:                     560 steps. Energy=    -537.4922044       time=       1.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.7028350  1.3656         -537.3372527 0.15495         -537.4922044   6.513   5.661  19.408   5.513
        *NEW* (Placed in 9)                                     Known (#7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 5_U and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0488 Dev= 0.00% S= 7.80 time= 0.28
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.50

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     597 steps. Energy=    -530.6427935       time=       1.45
 Minus side of path:                     657 steps. Energy=    -530.7625126       time=       1.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.6427935 0.87872E-02     -530.6340064 0.12851         -530.7625126   7.808   7.785   3.133  34.150
        Known (#5)                                              Known (#8)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     670.40    
 decide> The unconnected minima in the chain and their distances are:
     2        8.75     9 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3100 Dev= 0.13% S= 8.94 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         98
 DNEB run yielded 1 true transition state(s) time=   9.24

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     522 steps. Energy=    -538.7028350       time=       1.27
 Minus side of path:                     616 steps. Energy=    -539.6623457       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.7028350 0.23364         -538.4691953  1.1932         -539.6623457   9.486   8.756   7.216  14.827
        Known (#9)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -529.6554571 0.44458        -529.2108807  1.6778        -530.8886546   5.846   5.374  11.395   9.390
   2     -530.8886546  2.3078        -528.5808433  3.7500        -532.3308917  23.541   8.260   2.876  37.209
   5     -532.3308917  2.0907        -530.2401628 0.52235        -530.7625126  15.815  12.040   5.909  18.108
   7     -530.7625126 0.12851        -530.6340064 0.87872E-02    -530.6427935   7.808   7.785   3.133  34.150
   3     -530.6427935  1.7859        -528.8569192 0.13613        -528.9930536   8.369   7.876   2.249  47.569
   4     -528.9930536 0.45553E-01    -528.9475006  8.5447        -537.4922044  20.085  19.806   1.819  58.824
   6     -537.4922044 0.15495        -537.3372527  1.3656        -538.7028350   6.513   5.661  19.408   5.513
   8     -538.7028350 0.23364        -538.4691953  1.1932        -539.6623457   9.486   8.756   7.216  14.827

 Number of TS in the path       =      8
 Number of cycles               =      5

 Elapsed time=                                86.52
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             27313 time=          54.54 %= 63.0
 OPTIM> # of energy+gradient+Hessian calls=       316 time=          17.04 %= 19.7
