[gmx-users] Info regarding restrained minimization, equilibration & production

[Paolo Costa]

Dear Justin,

I thought too.
In case, could you please indicate me how I can constrain the interatomic
distance of a desired molecule, in such case the POM molecule?

Thanks a lot.

Paolo

Il giorno gio 7 mag 2020 alle ore 14:44 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

>
>
> On 5/7/20 8:41 AM, Paolo Costa wrote:
> > 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?
>
> That sounds to me like all interatomic distances were fixed via
> constraints, but you should contact the corresponding author to be sure,
> and ask for example inputs.
>
> -Justin
>
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-- 
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)