[gmx-users] Comm-mode

[Mark Abraham]

Hi,

Very many things are often simplified when you make a tutorial. Those .mdp
files are already complicated enough for a beginner.

Mark

On Mon, Mar 12, 2018 at 2:26 PM Amin Rouy <aminrou1986 at gmail.com> wrote:

> 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.
> >
> --
> 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.
>