[gmx-users] com motion and position restraints may cause artifacts

[Christos Deligkaris]

The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.....

Best wishes,

Christos Deligkaris, PhD

On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 1/16/20 5:17 AM, Alessandra Villa wrote:
> > Hi,
> >
> > On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris <deligkaris at gmail.com>
> > wrote:
> >
> >> dear all,
> >>
> >> I installed gromacs 2020 and I now get the following message during
> >> equilibration:
> >>
> >> NOTE 1 [file nvt.mdp]:
> >>
> >>    Removing center of mass motion in the presence of position
> >> restraints  might cause artifacts
> >>
> >> I do not recall seeing this with gromacs 2018. In which cases are
> >> artifacts created? Is it now recommended to not remove the center of
> >> mass motion during equilibration?
> >>
> >>
> > It is recommended not to have position restrain and remove of center of
> > mass at the same moment. That is also the case of the equilibration phase.
> > That may cause artifact depending on the system and the condition you are
> > simulating.
>
> What is the nature of these artifacts and where is this documented?
> Combining position restraints with COM motion removal is an extremely
> common practice. Phrases like "might cause artifacts" are troubling
> because that implies uncertainty. Are there cases when this combination
> does not cause artifacts?
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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