[gmx-users] Info regarding restrained minimization, equilibration & production
paolo.costa85 at gmail.com
Thu May 7 14:41:50 CEST 2020
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
Il giorno gio 7 mag 2020 alle ore 14:20 Justin Lemkul <jalemkul at vt.edu> ha
> 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
> > 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 A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
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> jalemkul at vt.edu | (540) 231-3129
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Paolo Costa, Ph.D.
Department of Chemistry and Biomolecular Sciences
University of Ottawa
10 Marie Curie, Ottawa, ON K1N 6N5, Canada
Room number: DRO 326 (D'Iorio Hall)
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