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

[Billy Williams-Noonan]

50 Angstroms between the solute and it's periodic image is a bit extreme.
Why is it rotating so quickly?  The rotational diffusion should happen
slowly

On Thu., 22 Aug. 2019, 12:52 pm Jorden Cabal, <jordencabal at gmail.com> wrote:

> Hi Justin,
> Thank you Justin for letting me know. I will definitely consider increasing
> the simulation box.
> Although, I was wondering that what would happen if I take
> comm-mode="Angular" and comm-grps= "molecule_AB !molecule_AB". This setting
> gives a warning which was ignored using -maxwarn option. After running 10
> ns of simulation, the system seems to be stable and very less fluctuations
> are observed upon visualization compared to when I use comm-mode="Linear".
> or nothing.
> What would you suggest? Should I proceed with the first setting?
> Thank you in advance.
>
> On Tue, Aug 20, 2019 at 9:25 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 8/20/19 5:21 AM, Jorden Cabal wrote:
> > > 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.
> >
> > You can apply biasing potentials to avoid rotation, but then you're
> > seriously perturbing the dynamics in a way that might completely bias
> > your results (I don't have nearly enough context to say for sure, so
> > I'll be a bit circumspect). If you have a large molecule that rotates,
> > you need a large box that reflects that intrinsic symmetry. It's the
> > same reason you can't build a long, rectangular box around a DNA duplex.
> > If it rotations orthogonal to the longest axis, it sees it's image and
> > the forces are invalid.
> >
> > There are no real "tricks" here. If you have a big molecule, you need a
> > suitably large box.
> >
> > -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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