[gmx-users] bonded interaction larger than cutoff

[Quyen Vu Van]

Thanks Dr. Lumkel

On Mon, Dec 17, 2018 at 2:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:

> On Mon, Dec 17, 2018 at 7:48 AM Quyen Vu Van <vuqv.phys at gmail.com> wrote:
>
> > Dear all,
> > I add a harmonic bond between two ends of my molecule (then my molecule
> > will have circle shape) with hope to calculate the force opens my
> molecule
> > (force the molecule straight).
> > Unfortunately, when this bond is quite big, gromacs said this bonded
> > interaction could not be calculated.
> > How can I overcome this? or is there any setup to calculate
> >
>
> Either do not use domain decomposition or use the pull code to bias the
> distance rather than trying to use a formal covalent bond.
>
> -Justin
> --
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> ==========================================
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> Justin A. Lemkul, Ph.D.
>
> Assistant Professor
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