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

[Paolo Costa]

Dear Justin

that means when I generate the topology file by pdb2gmx I will add manually
the section [constraints] on it?

Thanks.

Paolo

Il giorno gio 7 mag 2020 alle ore 14:50 Justin Lemkul <jalemkul at vt.edu> ha
scritto:

>
>
> On 5/7/20 8:47 AM, Paolo Costa wrote:
> > 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?
>
> Define [constraints] in the topology for all relevant interatomic
> distances.
>
> -Justin
>
> > 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
> >>
> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> jalemkul at 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-request at gromacs.org.
> >>
> >
>
> --
> ==================================================
>
> 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
>
> jalemkul at 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-request at 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)