VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Oct 21 2013 - 14:50:44 CDT

Hi Rodolfo,

It depends on what your aims are. If you want a transferrable set of
chlorobenzene parameters, that probably isn't a bad starting point for
simulations, and will yield parameters that are "close enough" with
minimal effort. If you were trying to get the most accurate parameter
set possible for chlorobenzene because the electron withdrawl by the
chlorine is something you believe is important to your work, it might be
worth looking at them again. It never hurts to check and see how
good/bad the values returned by paramchem are. I'd let FFTK set up all
the water interactions and just check with COLP if you are happy with
the convergence overall with the paramchem starting point (The water
interactions are the cheapest calculation in the grand scheme of
things). If not, you may consider letting the charges migrate from that
starting point, as while paramchem's algorithms get the general trends
right, you can usually improve the parameters if you spend a bit of time
optimizing the charges.

-Josh Vermaas

On 10/21/2013 10:43 AM, rodolfo gonzalez wrote:
> Ok, for example if I wanted to parametrize a chlorobenzene and lets
> assume that the paramchem penalties on all the atoms is below 10
> except for the Chlorine atom and the Carbon next to it. Then I would
> think that except for these two atoms, the rest are similar to the
> corresponding ones in benzene, and I would be tempted to keep the
> charges proposed by paramchem for those atoms while trying to
> parametrize only the ones with high penalty. Does it make any sense?
>
> Thanks
>
>
> On 21 October 2013 13:59, Norman Geist <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>
> What do you define as similar atoms?
>
>
>
> Norman Geist.
>
>
>
> *Von:*owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>
> [mailto:owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>]
> *Im Auftrag von *rodolfo gonzalez
>
>
> *Gesendet:* Montag, 21. Oktober 2013 08:58
> *An:* Norman Geist
> *Cc:* Namd Mailing List; vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
> *Betreff:* Re: vmd-l: fftk-charges
>
>
>
> Hi,
>
> Thanks a lot for your answer. I understand the point about the
> importance of the specific environment on the atomic charges of
> each molecule. However, I thought that for transferability reasons
> and for keeping consistency with the rest of the compounds in the
> CGenFF the charges of similar atoms should be kept the same. Isn't
> that the reason why the server paramchem provides penalties when
> looking for homologous parameters for a new compound?
>
> Thanks again for your reply, as I am new to this procedures, this
> kind of discussions are really helpful.
>
>
>
> On 21 October 2013 07:23, Norman Geist
> <norman.geist_at_uni-greifswald.de
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
>
> Hi,
>
>
>
> I don’t know if this is different in the charmm ff, but usually
> the partial charges are specific for compounds, or better called
> residues and not for atom types. Therefore one would usually
> compute the partial charges for a new residue from scratch for the
> whole molecule. I might be wrong here, but the partial charges
> depend a lot or almost only on the chemical environment. Means
> taking the charges from different molecules having a different
> chemical environment , is IMHO wrong.
>
>
>
> Norman Geist.
>
>
>
> *Von:*owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>
> [mailto:owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu>]
> *Im Auftrag von *rodolfo gonzalez
> *Gesendet:* Sonntag, 20. Oktober 2013 17:01
> *An:* vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
> *Betreff:* vmd-l: fftk-charges
>
>
>
> Hi,
>
> I am trying to parametrize a compound for which most atomic
> partial charges are already available in the CGenFF except for a
> few atoms. My question is: do I need to run the QM water-compund
> calculations for all the H-bond donors or acceptors atoms in my
> molecule or only for those whose atomic charge need to be
> parametrized?
>
> Thanks,
>
> Regards
>
>
>
>