[CP2K-user] [CP2K:11087] DFTB simulations of liquid water

[Guillaume Stirnemann]

Dear Thomas,

Thanks a lot for your comments. I ran quick tests following some of your
suggestions and I think I have figured out where the problem might come
from. It seems to be related with the use of damped gamma. I tried a short
simulation (20 ps) without the gamma scaling on and using the standard cp2k
parameters for SCC-DFTB, and everything seems fine. Now, this is very
strange because this did not seem to cause any problems when used in DFTB+
(JPCB 115, 6790 (2011)). Has anyone some experience with the use of damped
gamma in cp2k?

Thanks for pointing out some recent optimizations of the DFTB2 parameters
(by the way, in the files you sent the hh spl file seems to be missing,
right?). However, I would eventually need to perform simulations on
molecules containing atoms other than C, N, O or H, so I may have to stick
with a less-accurate set of parameters. Some more related questions below:

1) From what I understand, the spl files provided with cp2k corresponds to
the mio 0-1 parameter set. Is this right? Some parameters (e.g. for
phosphorus) seem to differ from the current mio 1-1 version.

2) For the molecules I am interested in, DFTB3-diag would probably be more
suitable. But the problem is that it was parametrized with the damped gamma
for hydrogens, for which there is the issue discussed above.

3) I would like to try to include the D3 corrections for dispersion
interactions. The only thing which is not clear to me is the values I have
to specify for D3_SCALING. Should I follow the values mentioned for the
zero-damping case in the DFTB+ manual (see
https://www.dftbplus.org/fileadmin/DFTBPLUS/public/dftbplus/latest/manual.pdf
p45)? However, they seem to correspond to full DFTB3, whereas cp2k only has
SCC-DFTB and DFTB3-diag. If anyone has experience regarding which
D3_SCALING to use in that case, this would be great.

Thanks again!

Best

Guillaume




On Thu, Dec 27, 2018 at 2:48 PM Thomas Kühne <tku... at gmail.com> wrote:

> Dear Guillaume,
>
> I have a couple of (hopefully helpful) comments using DFTB within CP2K:
> 1. To the best of my knowledge only the mio and znorg parameter sets,
> i.e. the ob2 parameter set needs to be downloaded from dftb.org
> 2. IMHO, the usage of a damped gamma does not represent a general
> improvement, it marginally improves the 1st peak for water but appears
> to be worse for a lot of other systems
> 3. I rather suggest to use the improved parametrization of Dömer et al.,
> see e.g. https://arxiv.org/pdf/1408.5161.pdf and references therein.
> Since I couldn’t find the files anywhere else, I have attached them to the
> present email. We will check them again and upload them to the repository
> next week.
> 4. For comparison have a look at Fig. 1-3 in
> https://arxiv.org/pdf/1512.08206.pdf
> for a plain DFTB calculation of liquid water by CP2K with the provided
> original
> parametrization, without the modified gamma and no vdw correction, but
> including
> nuclear quantum effects. No inhomogeneity in the particle density have
> been observed.
> 5. Please also have a look at the recent discussion about the SPME
> settings,
> which may play a role in your observed behavior.
>
> Best,
> Thomas
>
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> Am 26.12.2018 um 16:33 schrieb Guillaume Stirnemann <gsti... at gmail.com>:
>
> Hi all,
>
> I am trying to simulate a box of liquid water using DFTB with periodic
> boundary conditions. My initial configuration is taken from a previous
> classical MD run performed in the NVT ensemble at the experimental density.
> I have tried different set-ups, including SCC-DFTB ("DFTB2") and
> DFTB3-diag, both with or without Grimme's D3 corrections, all ran in the
> NVT ensemble for 50 ps.
> In all cases, the simulations run well, but I end-up with a large hole in
> the simulation box. When comparing my radial distribution functions that of
> Cui who used DFBT+ (JPCB 115, 6790 (2011)), the first peak of the O-H rdf
> is usually a bit more pronounced but the contraction of the whole system is
> more visible on the second hydration shell. The differences are less
> visible for the O-O rdfs. The hole occupies about 1/2 of the simulation
> box, so the final density of my liquid phase is about 2!
>
> I attach the initial configuration, and the cp2k input file for DFTB2 with
> no D3. I tried on two different machines, one with 6.1 and the other one
> with 5.1.
>
> I am not an expert of CP2K so there might be some issues with my input,
> and your help would be very much appreciated.
>
> Best wishes
>
> Guillaume
> CNRS Institut de Biologie Physico-Chimique, Paris, France
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> <input-DFTB2-gamma-noD.in><h2o.xyz>
>
>
> ==============================
> Prof. Dr. Thomas D. Kühne
> Dynamics of Condensed Matter
> Chair of Theoretical Chemistry
> University of Paderborn
> Warburger Str. 100
> D-33098 Paderborn
> Germany
> tdku... at mail.upb.de
> +49/(0)5251/60-5726
>
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