Dear Justin,

thanks a lot for your valuable information.
The system (Keggin anion, POM) I am trying to simulate is almost identical
to the one already studied in literature (doi: 10.1021/jp077098p).
In the SI of this work, the authors stated "*Keggin anions are treated as
rigid particles thus keeping constant the distances between the different
metal and oxygen atom".*
That means they did not parametrize the bonded interactions for such
molecule, isn't?

Thanks.

Paolo

Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul <jalem...@vt.edu> ha
scritto:

>
>
> On 5/6/20 11:35 AM, Paolo Costa wrote:
> > Dear Gromacs users,
> >
> > I am interested on studying the interaction between large metal cluster
> > anions (polyoxometallates, POM) with different organic cations (e.g
> > perylenes, etc..) in water.
> > I have already the non bonded parameters of POMs from literature, while
> the
> > bonded parameters I calculated from Gaussian and VFFDT software.
> > If I do not apply a position restraining force on the POM atoms, the POM
> > structure gets distorted too much from the experimental one. I guess this
> > is due to the lack of a good force field parametrization for
> > metal-containing compound.
> > *Thus, my question is the following:*
> > *can I keep applying a position restraining force on POM atoms during the
> > minimization, equilibration and production steps or is it conceptually
> > wrong?*
>
> If you're restraining a configuration because the force field is so bad,
> I'd immediately be skeptical of the quality of any simulation. Bonded
> parameters are generally easy to reproduce and probably aren't the
> source of your problem if you've implemented them carefully, but if
> you're trying to combine new bonded parameters with existing nonbonded
> parameters, you need to do careful validation on a known system.
>
> If your system doesn't work, you should back up and make sure you can
> reproduce a published study using the same parameters and not ones of
> your creation.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
Paolo Costa, Ph.D.
Postdoctoral Researcher
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to