[gmx-users] bonded interaction larger than cutoff

Justin Lemkul jalemkul at vt.edu
Mon Dec 17 14:29:49 CET 2018

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 A. Lemkul, Ph.D.

Assistant Professor

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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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