
 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 11:58:14
  [-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 = 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


 KeyInt>> Using natural internal coordinates. # of coords =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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=    -534.6711754     RMS force=    0.9676615577E-06
 OPTIM> Final energy  =    -528.7249325     RMS force=    0.7703196372E-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=     27779.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.29     1 
 

 tryconnect> 315-iteration DNEB run for minima 1_S and 2_F using 9 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 315 RMS= 0.2395 Dev= 2.14% S= 36.82 time= 5.77
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):         59
 Converged to TS (number of iterations):         44
 DNEB run yielded 2 true transition state(s) time=  11.61

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     653 steps. Energy=    -534.5278451       time=       1.65
 Minus side of path:                     749 steps. Energy=    -535.3372163       time=       1.97

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5278451  3.4847         -531.0431372  4.2941         -535.3372163  17.765  10.837  12.495   8.563
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1086 steps. Energy=    -534.1997122       time=       3.34
 Minus side of path:                     612 steps. Energy=    -528.7249325       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122  7.0282         -527.1714739  1.5535         -528.7249325  27.158  25.232   2.964  36.099
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     571.04    
 decide> The unconnected minima in the chain and their distances are:
     5        7.38     3     4        5.53     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1075 Dev= 0.08% S= 7.43 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=   4.90

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     573 steps. Energy=    -534.7851393       time=       1.41
 Minus side of path:                     532 steps. Energy=    -534.5864911       time=       1.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7851393 0.27820         -534.5069412 0.79550E-01     -534.5864911   5.365   5.094   3.423  31.262
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.7760 Dev= 0.78% S= 6.20 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.70

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     562 steps. Energy=    -534.5278451       time=       1.37
 Minus side of path:                     561 steps. Energy=    -534.6711754       time=       1.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.5278451 0.77536E-01     -534.4503089 0.22087         -534.6711754   3.471   3.384   4.946  21.633
        *NEW* (Placed in 8)                                     Known (#1)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      3 missing connections, weight=     262.15    
 decide> The unconnected minima in the chain and their distances are:
     5        5.12     7     6        3.23     3     4        4.56     8 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_U using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2526 Dev= 0.14% S= 5.51 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   2.47

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     563 steps. Energy=    -534.1997122       time=       1.37
 Minus side of path:                     573 steps. Energy=    -534.5864911       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.1997122 0.78097E-01     -534.1216152 0.46488         -534.5864911   5.520   5.120  19.578   5.465
        Known (#5)                                              Known (#7)
 Unconnected minimum 7 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 3_U and 6_F using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1231 Dev= 0.02% S= 3.27 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         13
 DNEB run yielded 1 true transition state(s) time=   2.35

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     570 steps. Energy=    -534.7851393       time=       1.44
 Minus side of path:                     560 steps. Energy=    -534.5278451       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7851393 0.32238         -534.4627563 0.65089E-01     -534.5278451   3.328   3.225   9.808  10.909
        Known (#6)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 4_F and 8_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.5497 Dev= 0.87% S= 5.02 time= 0.31
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.05

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     563 steps. Energy=    -534.7851393       time=       1.41
 Minus side of path:                     561 steps. Energy=    -534.5278451       time=       1.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7851393 0.32238         -534.4627563 0.65089E-01     -534.5278451   3.328   3.225   9.808  10.910
        *NEW* (Placed in 9)                                     Known (#8)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     33.134    
 decide> The unconnected minima in the chain and their distances are:
     4        3.21     9 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 9_S using 2 images  (DNEB attempt #1)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.8804 Dev= 0.60% S= 3.84 time= 0.31
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=   5.43

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     614 steps. Energy=    -534.7851393       time=       1.52
 Minus side of path:                     509 steps. Energy=    -533.9424843       time=       1.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7851393 0.95915         -533.8259940 0.11649         -533.9424843   8.491   8.137   2.677  39.966
        Known (#9)                                              *NEW* (Placed in 10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      1 missing connections, weight=     66.268    
 decide> The unconnected minima in the chain and their distances are:
     4        3.21     9 
 

 tryconnect> 245-iteration DNEB run for minima 4_F and 9_S using 7 images  (DNEB attempt #2)  ...
 Finished simple initial interpolation
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 245 RMS= 0.2081 Dev= 6.31% S= 4.94 time= 3.51
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):          9
 DNEB run yielded 1 true transition state(s) time=   1.87

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     586 steps. Energy=    -534.7851393       time=       1.44
 Minus side of path:                     510 steps. Energy=    -535.3372163       time=       1.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7851393  8.2209         -526.5642444  8.7730         -535.3372163   4.933   3.212   7.330  14.597
        Known (#9)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -534.6711754 0.22087        -534.4503089 0.77536E-01    -534.5278451   3.471   3.384   4.946  21.633
   7     -534.5278451 0.65089E-01    -534.4627563 0.32238        -534.7851393   3.328   3.225   9.808  10.910
   9     -534.7851393  8.2209        -526.5642444  8.7730        -535.3372163   4.933   3.212   7.330  14.597
   1     -535.3372163  4.2941        -531.0431372  3.4847        -534.5278451  17.765  10.837  12.495   8.563
   6     -534.5278451 0.65089E-01    -534.4627563 0.32238        -534.7851393   3.328   3.225   9.808  10.909
   3     -534.7851393 0.27820        -534.5069412 0.79550E-01    -534.5864911   5.365   5.094   3.423  31.262
   5     -534.5864911 0.46488        -534.1216152 0.78097E-01    -534.1997122   5.520   5.120  19.578   5.465
   2     -534.1997122  7.0282        -527.1714739  1.5535        -528.7249325  27.158  25.232   2.964  36.099

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

 Elapsed time=                                74.95
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             22084 time=          44.52 %= 59.4
 OPTIM> # of energy+gradient+Hessian calls=       285 time=          15.49 %= 20.7
