Elstner_DFTB_Excercise - Optimize all structures with the...

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Introduction into DFTB Marcus Elstner August 7, 2006 1 Geometry optimization 1Waterdimer : Optimize the structures of the three water dimers wat1.gen, wat2.gen and wat3.gen. Use cgr for that (option 4) and view the result with molden. What is the energy difference and what is the dimer binding energy? Use steepest descent for that (option 3) Do the same for the strongly H-bonded systems in 2Stronghbonds : what are the binding energies compared to the water dimer? 3Watercluster : Optimize the waterclusters and calculate the binding energy of every one: Plot the binding energy vs. cluster size. Use the shell script ’R’ to achieve this. Simple peptides: 4peptides Use the script from 3Watercluster to convert the peptide struc- tures to xyz-format: view them with molden.
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Unformatted text preview: Optimize all structures with the script and look at the relative energies. Are all conformers stable? 2 Dispersion Dispersion: do the examples in 5DISPERSION-example 1 6DNAbasepairs : Optimize the structures with and without dispersion. What do you nd? 7benzene: optimize with and without dispersion. 8peptides: Only do single point energies with Dispersion for the struc-tures and for those of 4peptides. Get a feeling, at which size dispersion starts to matter. 3 Vibrational frequencies Calculate the vibrational frequencies of water in 10vib/h2o . 4 MD Look at the inputle doh.dyn in 11MD . After running, move all out.gen*v to another place, and then run Rcollect to get the trajectory XMO. 2...
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Elstner_DFTB_Excercise - Optimize all structures with the...

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