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

[Jorden Cabal]

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
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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