[CP2K-user] [CP2K:15704] Wrong water density wih xTB

Pedro Maximiano pedro... at gmail.com
Thu Jul 8 17:31:41 UTC 2021

Dear Guillaume

Thank you very much for your reply and for sharing that information.
I will try to run the calculations with SCC-DFTB and the water parameters 
you mentioned.

Best regards

On Thursday, July 8, 2021 at 4:25:11 PM UTC+1 gs... at gmail.com wrote:

> Dear Pedro, 
> Unfortunately, this is a known issue with tight-binding methods such as 
> DFTB or xTB. It has been reported before, see e.g. 
> https://pubs.acs.org/doi/abs/10.1021/jp400953a, although it does not seem 
> to be widely communicated. This info had been nicely shared by Thomas Kühne 
> and Juerg Hutter here some time ago (see Dec 2018). 
> Systems shrink unreasonably in the NPT ensemble, and usually, bubbles 
> appear if the volume is kept constant to satisfy the experimental density. 
> It is pretty clear by looking at the radial distribution functions that the 
> structure is usually pretty badly reproduced. 
> In my group we did many many tests using different generations of TB 
> methods in cp2k, including xTB. The only set of parameters that seem to 
> give "stable" results for water (in the NVT ensemble) are the SCC-DFTB, 
> sometimes called DFTB2, using the mio-1-1 parameter set. Thomas also shared 
> some parameters that were reoptimized to better reproduce water structure, 
> see in https://arxiv.org/pdf/1408.5161.pdf. 
> These parameters do not lead to voids in the simulation box, but I never 
> tested them in NPT. 
> It seems that later generations of xTB seem give much more accurate 
> results in general (no idea how they behave for liquid water), but I don't 
> think they are currently implemented in cp2k. 
> Best wishes, 
> Guillaume Stirnemann 
> On Wed, Jul 7, 2021 at 7:01 PM Pedro Maximiano <pe... at gmail.com> wrote:
>> Dear CP2K users and developers
>> I'm a relatively new CP2K user, and I'm trying to do MD simulations of a 
>> dimer of a small molecule in water with the GFN-xTB method. To prepare the 
>> simulations I first minimize and then equilibrate the boxes in a NPT 
>> ensemble (300 K, 1 bar) with the AMBER force field, followed by a short NVT 
>> run (also with AMBER FF). I then start the xTB simulation from the final 
>> point of the classical MD run, in the NVT ensemble (300 K).  However, I 
>> noticed that voids appear in the xTB simulation boxes, probably indicative 
>> of a wrong system density.
>> To reproduce the issue in a simpler system, I ran a NPT simulation with 
>> xTB (300 K, 1 bar) on a box of 126 water molecules in CP2K. The box was 
>> pre-equilibrated in a NPT run (also 300 K, 1 bar), with the AMBER FF TIP3P 
>> parameters, yielding a density of 1.023 g/cm3. This box was then subjected 
>> to a minimization and a short NVT equilibration with xTB, prior to the NPT 
>> equilibration. Indeed, I observed that the xTB NPT run compressed the box, 
>> to a final density of 1.481 g/cm3.
>> I'm attaching here the input for the xTB NPT simulation of water. The 
>> sections that are commented are settings which I also tried, without 
>> success, namely:
>> - Adding a NONBONDED potential to xTB (taken from the test file 
>> xTB/regtest-debug/h2o-atprop_nonbonded.inp)
>> - Changing the settings in the POISSON/EWALD section to non default 
>> values (up to RCUT = 10.0 Angstrom)
>> Note that I also ran the test xTB/regtest-debug/h2o-atprop_nonbonded.inp 
>> for 20000 steps and obtained an abnormally high density (1.722 g/cm3).
>> All runs were performed in CP2K v8.2, but I also noticed the same issues 
>> when running in version 7.1.
>> Could you please take a look at the input file and tell me if I'm missing 
>> something?
>> Best regards
>> Pedro Maximiano 
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