OPTIM version Unversioned directory, 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> OPTIM is running on host name
nest.ch.private.cam.ac.uk
getparams> Number of atoms (or variables) determined as 220
getparams> Number of optimisation degrees of freedom 660
keyword> Distance tolerance for distinguishing atoms in the same orbit= 0.06000
keyword> Maximum number of secondary sets in perm.allow file= 5
keyword> Number of groups of permutable atoms= 25
keywords> input coordinates for AMBER20 system will be read from start
keywords> reading in xyz format
chirality init> Number of bonds: 227
find_cistrans> 11 peptide bonds detected
find_chiral> 13 chiral atoms found
keywords> Set frequency conversion factor to the AMBER default value: 20454830000000.000
keywords> This corresponds to frequencies being given in radians/s
fetchz> Hybrid EF/BFGS transition state search, maximum steps= 10000
maximum tangent space steps= 20 or 200 when overlap is better than 0.999900
fetchz> Uphill mode is 0 for initial step and 0 after that
fetchz> No Hessian: Rayleigh-Ritz max steps=1000 RMS < 0.0100 and |% change|< 1.0
fetchz> Hessian eigenvector in Rayleigh-Ritz scheme calculated using method 2
fetchz> 660 Cartesian coordinates will be optimised for 220 atoms
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> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 60000
fetchz> Maximum energy rise in LBFGS minimization= 0.1000000000E-03
fetchz> Number of updates in LBFGS= 1500
fetchz> Number of updates in XLBFGS= 4
fetchz> Number of updates in mind= 4
fetchz> Initial guess for diagonal elements in LBFGS= 0.1000
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= -454.4730096 RMS force= 0.9945547350E-06
OPTIM> Final energy = -453.1781331 RMS force= 0.9785362311E-06
OPTIM> finish endpoint passed chirality check
OPTIM> finish endpoint cis/trans consistent with starting geometry
KeyConnect> Maximum cycles = 5, maximum images = 30
KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 0.50
KeyConnect> Image density = 2.00, iteration density = 20.00
KeyNEB> Initial and final NEB force constants 10.00000000 10.00000000 factor= 1.000000000
KeyNEB> Number of images will vary depending on the separation of the endpoints
KeyNEB> NEB coordinates will be saved to xyz file "neb.xyz" every 100 iterations
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 0.01
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 Exp[D]
>>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
decide> Shortest path in Dijkstra has 1 steps with 1 missing connections, weight= 584.36
decide> The unconnected minima in the chain and their distances are:
2 6.37 1
tryconnect> 240-iteration DNEB run for minima 1_S and 2_F using 12 images (DNEB attempt #1) ...
rwg> NEB coordinates were saved to xyz file "neb.0.xyz"
rwg> NEB coordinates were saved to xyz file "neb.100.xyz"
rwg> NEB coordinates were saved to xyz file "neb.200.xyz"
rwg> NEB coordinates were saved to xyz file "neb.0.xyz"
Time to go through NEB: 9.5558600000000009
Double-ended search iterations= 240 RMS= 0.0600 Dev= 1.34% S= 6.70 time= 9.56
Following 1 images are candidates for TS: 6
Converged to TS (number of iterations): 8
DNEB run yielded 1 true transition state(s) time= 4.64
Energies:
-452.44826809254778
>>>>> Path run for ts 1 ...
Plus side of path: 937 steps. Energy= -453.1781331 time= 3.68
Minus side of path: 864 steps. Energy= -454.4730096 time= 3.33
E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
-453.1781331 0.72987 -452.4482681 2.0247 -454.4730096 6.757 6.371 12.642 17.402
Known (#2) Known (#1)
output> Connected path found
ts E+ Ets - E+ Ets Ets - E- E- S D gamma ~N
1 -454.4730096 2.0247 -452.4482681 0.72987 -453.1781331 6.371 6.371 12.642 17.402
Number of TS in the path = 1
Number of cycles = 1
Elapsed time= 45.01
OPTIM> # of energy calls= 0 time= 0.00 %= 0.0
OPTIM> # of energy+gradient calls= 6439 time= 18.86 %= 41.9
OPTIM> # of energy+gradient+Hessian calls= 3 time= 23.54 %= 52.3