Dear Paul, Thanks for the test set! (Usually, it's sufficient to post the files somewhere and paste in the URL or use a .tar.bz2)
To confirm - the idea is that the COF files were used to generate the MOL2 files with the associated QEq charges. As far as I know, many people use the same approximation for n=4 orbitals and above with Slater-type orbitals. I probably won't have time for a while, but I'd like to re-visit QEq charges while I work to implement the new PQEq polarizable charge models from the Goddard group. (I have a not-so-secret desire to see a UFF-like force field with a polarizable charge model.) Thanks again, it's a big help. -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ > On Mar 5, 2019, at 3:34 PM, Paul Becherer <paul.beche...@culgi.com> wrote: > > Dear Geoff, > > As promised, here are the molecules we internally used for testing and > validation of our QEq implementation. I've attached them as a tar file > containing files in COF and MOL2 format. I tried a zip file first but > apparently that extension is blacklisted for the mailing list. I hope the > .tar file will work, and my apologies if you receive this twice. > > The results are divided into three categories: > > * Metal halides (covering Table II in the Rappé and Goddard paper; we used > lambda = 0.5) > * Molecules (covering Tables III and (partially) IV) > * NaCl clusters (covering Figure 6) > > We took some care to use the geometries from the references given in the > paper. > > For atoms with a principal quantum number of n = 4 and higher, the analytical > expressions we use for the Coulomb integrals become numerically unstable. For > those cases we use a rescaling to n = 3 (using equation 17 from Rappé and > Goddard). For molecules involving those atoms, the deviations from the values > in the literature are thus slightly higher. > > The only molecules, as far as I know, with charges that really do not match > those in the QEq paper of Rappé and Goddard, are lithium hydride (LiH) and > silane (SiH4). > > For SiH4 I suspect that there's an error in the table, and that the hydrogen > charges reported for silane actually belong to the molecule directly above > that in Table IV, which is ketene, H2C=C=O. > > For LiH I don't know what the problem is. Any change to the parameters or > functional forms for hydrogen will change the hydrogen charges on other > molecules so that *they* no longer match, so I could not find a way to > reproduce the LiH charges. > > Kind regards, > > > Paul Becherer > Development Scientist > > Culgi B.V. > Galileiweg 8 > 2333 BD Leiden > The Netherlands > +31-71-332-2056 > > -----Original Message----- > From: Geoffrey Hutchison <geoff.hutchi...@gmail.com> > Sent: Saturday, March 02, 2019 23:14 > To: Paul Becherer <paul.beche...@culgi.com> > Cc: openbabel-discuss@lists.sourceforge.net > Subject: Re: [Open Babel] Contributed code for new file format > >> Looking at it again now, it seems that the charges from Open Babel's QEq >> often have the wrong sign or are simply unreasonably large. I have no idea >> what causes that, as I only had a cursory look at the code. But it looks as >> if there's more going on than just the additional simplifications to QEq: >> even the QTPIE charges do not seem to reproduce those from the QTPIE paper >> by Chen and Martinez (e.g. the charges on phenol as reported in the preprint >> on arXiv, https://arxiv.org/abs/0807.2068 ). I cannot rule out that I've >> used the charge model options in the wrong way, but they seemed quite >> straightforward. > > Ironically, the code for both QEq and QTPIE in Open Babel were contributed by > Chen. But I've heard similar things about the signs and magnitudes of the QEq > charges. Naturally, considering the source of the code, I didn't question the > results at the time, but it's been several years with off-and-on questions > about it. > >> I can send the molecule geometries that we used in validating our QEq >> against the Rappé and Goddard article, if that would be of help, or run our >> QEq implementation on a set of molecules of your choice and send back the >> results. Our coverage of elements is limited to that in the original paper, >> which covers H, Li, C, N, O, F, Na, Si, P, S, Cl, K, Br, Rb, I, Cs. > > If you're willing to send some molecule geometries and charges, that would be > very helpful. I probably won't have time to evaluate the code until the > summer, but having a validation set would be a helpful contribution. > > Incidentally, I've been following the work by the Goddard group on their new > polarizable QEq model (e.g., PQEq2) and I'm trying to get a test set together > for an independent implantation of those. > > -Geoff > <QEQ_results.tar>
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