[gmx-users] "comm-mode = Angular" gives error

[Jorden Cabal]

Hi Justin,
Thank you for your response. In my case the cost of increasing simulation
box is very large. I have already tried it by keeping distance between the
periodic images of the macromolecule up to 50 Angstrom. Could you suggest
me any other option to do this. In Gromacs, rotation around pivot can be
enforced, is it possible to use this method somehow to counter the
rotation? Even if its possible, how and to which extent do you think it
will add biasness to the independent behavior of the macromolecule. Any
suggestions, comments in this regard will help me.
Thank you

On Mon, Aug 19, 2019 at 8:00 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/19/19 12:39 AM, Jorden Cabal wrote:
> > Dear Users,
> > I am trying to perform simulation of a very large and complex system and
> > which requires me to make the simulation box rectangular cube instead
> (box
> > dimension 24.5 nm * 12.5 nm * 12.3 nm) of perfect cuboid in order to
> > minimize the number of atoms present in the system.
> >
> > I am facing the problem of interaction between periodic images due to
> > rotational movement of the macro molecule. I have tried lowering the
> > *nstcomm* (frequency of removal of center of mass velocity) to 10 and it
> > seems it might work but the speed become very slow because it also
> requires
> > *nstcalcenergy* to 10.
> >
> > When I use *comm-mode="Angular"* with *comm-grps="system" *it says "*too
> > many warnings*" and the warning is
> > *"Removing the rotation around the center of mass in a periodic system,
> > this can lead to artifacts. Only use this on a single (cluster of)
> > molecules. This cluster should not cross periodic boundaries*"
> >
> > *"Although this problem can be ignored using -maxwarn option in the
> grompp
> > command. I want to know that if that is the correct thing to do?" *
> >
> > *Instead, *I have also tried to work this out by changing the* comm-grps=
> > "Protein" *but then it throws two warnings first being the same as
> > mentioned above and the second warning says "*Some atoms are not part of
> > any center of mass motion removal group. This may lead to artifacts. In
> > most cases one should use one group for the whole system*"
> >
> > Again this can be ignored using -maxwarn option but is that right to do?
> > Please suggest me regarding this.
>
> This is not the purpose of comm-mode/comm-grps, which account for net
> COM motion as a function of other errors in the simulation (Google the
> "flying ice cube effect"). You can't prevent your molecules from
> rotating in any physically realistic way. The simulation box needs to be
> larger to avoid these interactions, and comm-mode/comm-grps is not the
> way to get around it.
>
> -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
>
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