[DFTB-Plus-User] DFTB+ incorrect density in MD for water

[Bálint Aradi]

Dear Luca,

sorry, indeed, your previous post apparently went done between other
threads. In that case, it is OK to re-post, for sure. And your post was
definitely as specific as it can be. :-)

I am not an MD and water expert, but here a few comments, which may help
you, nevertheless.

* When using the 3ob set, make sure to use HCorrection / Damping and
ThirdOrderFull options.

* The Berendsen-barostat we have implemented is known for fluctuating a
lot, but I have no clue, how severe it would be with water and which
time scale to look for (maybe somebody more expert in MD can comment on
that).

* I think, dispersion may indeed be important.

* Last, not least, the water description with the DFTB Hamiltonian is
not really wonderful, mostly due to the missing multipoles in the model.
So, it may sense, as done in

https://pubs.acs.org/doi/full/10.1021/jp1010555

to get the water box initial geometry from somewhere else, and do NVT
afterwards.

* Depending, what you are after, you could also test the xTB Hamiltonian
in DFTB+.

Best regards,

Bálint


On 28.06.22 12:07, Luca Babetto wrote:
> Dear all,
> 
> I apologise for this duplicate message, but my previous post has gone
> unanswered and I don't know if it was just lost amongst the various
> threads, so I'm reposting the message. I hope this does not come across
> as disrespectful, I greatly appreciate all the work the volunteers in
> the DFTB+ community put in to help users resolve these issues and I am
> well aware that support is not "owed" to us but simply granted by your
> kind souls! 😄
> 
> I'm trying to run a MD simulation on a water box using the 3ob parameter
> set. I constructed a 200 molecules water box with packmol and I used the
> following input file to run the MD simulation:
> 
> Geometry = GenFormat {
>   <<< "water_bulk.gen"
> }
> 
> Driver = VelocityVerlet{
>   TimeStep [fs] = 1.0
>   Thermostat = NoseHoover {
>     Temperature [Kelvin] = 298
>     CouplingStrength [cm^-1] = 3200
>   }
>   Barostat = {
>     Pressure [Pa] = 101325.0
>     TimeScale [ps] = 0.01
>   }
>   Steps = 400000
>   MovedAtoms = 1:-1
>   MDRestartFrequency = 1000
> }
> 
> Hamiltonian = DFTB {
>   Scc = Yes
>   SlaterKosterFiles = Type2FileNames {
>     Prefix = "3ob/3ob-3-1/"
>     Separator = "-"
>     Suffix = ".skf"
>   }
>   kPointsAndWeights = { 0.0 0.0 0.0 1.0 }
>   MaxAngularMomentum {
>     O = "p"
>     H = "s"
>   }
> }
> 
> ParserOptions {
>   ParserVersion = 11
> }
> 
> I'm using periodic conditions with a 18.32 Angstrom box, for a starting
> cell volume of 6411.22 Angstrom^3 and a starting density of 973.75 g/L.
> I know I'm using a relatively low TimeScale value for the barostat, but
> I just wanted to quickly equilibrate the system and then run a
> production simulation.
> 
> My problem is that with these settings, the box keeps expanding and thus
> the density keeps decreasing. I stopped the simulation after 100ps
> because I saw that the volume kept expanding (linearly, with no sign of
> reaching an equilibrium value) until a final value of 6460.63
> Angstrom^3, for a density of 926.06 g/L which is just too far away from
> the experimental value for me to use.
> 
> I tried rerunning the calculation with the recommended settings for the
> barostat TimeScale value (0.1 ps), the same result occurs, just an order
> of magnitude slower as I would expect.
> 
> Am I using some incorrect settings? Is there a problem with the
> barostat, or maybe with the 3ob parametrization? Is DFTB simply not
> designed to reprocude the correct density for a water box so I should
> just set the "correct" volume and run NVT as I've seen done in the
> literature a few times? Should I include dispersion corrections
> explicitly via DFT-D3? Any pointer is greatly appreciated, thank you!
> 
> Please let me know if you need more information on my calculation setup,
> 
> Kind regards
> 
> Luca
> 
> _______________________________________________
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-- 
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/

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