[CP2K-user] [CP2K:11088] DFTB simulations of liquid water

[Thomas Kühne]

Dear Guillaume, 

as written in the paper only modified O-O & O-H parameter sets were 
provided, i.e. the H-H interactions should be taken from the original mio 
parameter set. To the best of my knowledge, the latter is indeed the 
0-1 version. 

Best, 
Thomas

> Am 28.12.2018 um 17:06 schrieb Guillaume Stirnemann <gsti... at gmail.com>:
> 
> 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 <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 <mailto: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 <http://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 <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 <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 <mailto: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 <http://input-dftb2-gamma-nod.in/>><h2o.xyz <http://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 <mailto:tdku... at mail.upb.de>
> +49/(0)5251/60-5726
> 
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