[gmx-users] Comm-mode

[Amin Rouy]

But, why in some Gromacs tutorial there is no comm-mode used in .mdp file,
for example in 'Lysozyme in water';

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html

On Mon, Mar 12, 2018 at 1:50 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you get this wrong, the equipartition of energy is usually broken and
> the simulation is probably unphysical.
>
> Mark
>
> On Mon, Mar 12, 2018, 13:47 Amin Rouy <aminrou1986 at gmail.com> wrote:
>
> > Dear Justin,
> >
> > If we do not use comm-mode, which quantity might be changed after
> > simulations?
> >
> > Can we remove center of mass after the simulation done?
> >
> > On Sat, Mar 10, 2018 at 6:36 PM, Amin Rouy <aminrou1986 at gmail.com>
> wrote:
> >
> > > thank you so much.
> > >
> > > On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >
> > >>
> > >>
> > >> On 3/10/18 12:31 PM, Amin Rouy wrote:
> > >>
> > >>> Thank you Justin.
> > >>> What if we do not know the phase of the final result? of if we are
> in 2
> > >>> phase region (gas-liquid)
> > >>>
> > >>
> > >> If you're applying PBC you have to use linear as your comm-mode
> (grompp
> > >> will fail otherwise, so that's a pretty good hint).
> > >>
> > >> -Justin
> > >>
> > >>
> > >> On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > >>>
> > >>>
> > >>>> On 3/10/18 12:17 PM, Amin Rouy wrote:
> > >>>>
> > >>>> Dear Gromacs people,
> > >>>>>
> > >>>>> I have a question please.
> > >>>>>
> > >>>>> In which condition we must use center of mass removal? Is that
> > >>>>> optional or
> > >>>>> necessary?
> > >>>>>
> > >>>>> Typically necessary.
> > >>>>
> > >>>> and how to know which mode (linear or angular) is better for our
> > >>>>
> > >>>>> simulations?
> > >>>>>
> > >>>>> Linear is only for condensed-phase systems, angular is only for
> > vacuum
> > >>>> simulations.
> > >>>>
> > >>>> -Justin
> > >>>>
> > >>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> Justin A. Lemkul, Ph.D.
> > >>>> Assistant Professor
> > >>>> Virginia Tech Department of Biochemistry
> > >>>>
> > >>>> 303 Engel Hall
> > >>>> 340 West Campus Dr.
> > >>>> Blacksburg, VA 24061
> > >>>>
> > >>>> jalemkul at vt.edu | (540) 231-3129
> > >>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >>>>
> > >>>> ==================================================
> > >>>>
> > >>>> --
> > >>>> 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
> > >> Virginia Tech Department of Biochemistry
> > >>
> > >> 303 Engel Hall
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at vt.edu | (540) 231-3129
> > >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >>
> > >> ==================================================
> > >>
> > >> --
> > >> 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.
> > >>
> > >
> > >
> > --
> > 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.
> >
> --
> 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.
>