<div><p>I’m completely new to cp2k and have only just
installed it today, because I learned that it was used to generate the
MD17 dataset, which I am interested in.</p>
<p>I’m currently starting up a neural network approach to molecular
dynamics and for that I need a dataset. The ideal dataset for my
research is essentially the MD17 dataset found <a href="http://www.quantum-machine.org/datasets/#md-datasets">here <span>1</span></a>:
However, there is a problem with this dataset for my use-case, as
quoted in the originating article, the MD17 dataset is created as:</p>
<span>
<p>"The data used for training the DFT models were created running abinitio MD in the NVT ensemble using the Nosé-Hoover ther-
mostat at 500 K during a 200 ps simulation with a resolution of 0.5 fs. We computed forces and energies using all-electrons at the generalized gradient approximation level of theory with the Perdew-Burke-Ernzerhof (PBE) 65 exchange-correlation functional, treating van der Waals interactions with the Tkatchenko-Scheffler (TS) method 66 . All calculations were performed with FHI-aims 67 . The final training data was generated by subsampling the full trajectory under preservation of the Maxwell-Boltzmann distribution for the energies.<br>
To create the coupled cluster datasets, we reused the same geometries as for the<br>
DFT models and recomputed energies and forces using all-electron coupled cluster<br>
with single, double, and perturbative triple excitations (CCSD(T)). The Dunning’s<br>
correlation-consistent basis set cc-pVTZ was used for ethanol, cc-pVDZ for toluene<br>
and malonaldehyde and CCSD/cc-pVDZ for aspirin. All calculations were<br>
performed with the Psi4 68 software suite."</p>
</span>
<p>So the data has been subsampled, meaning that the datapoints in the
MD17 dataset do not have the same time-step size between two following
data samples, which is needed for my work.</p>
<p>So my question are:<br>
Is there anyway of generating this dataset again given the above
information? I have tried contacting the author, but haven’t heard
anything back yet.</p>
<p>Or alternatively, are there any other simple systems like this
available online or does anyone have any scripts/tutorial for how to
generate a realistic molecular system dataset.<br>
What I need are the atomic positions at each step, and ideally I would
like the atomic velocities and Force vectors as well if possible. I
would like to generate at least 100k-500k time-steps since I need quite a
lot of data for the neural network training.</p>
<p>Any insight from experienced cp2k users or people in the field of molecular dynamics would be greatly appreciated.</p></div>