[gmx-users] Comm-mode

[Mark Abraham]

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
> >>>>
> >>>> ==================================================
> >>>>
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> >> --
> >> ==================================================
> >>
> >> 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
> >>
> >> ==================================================
> >>
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