[gmx-users] Constraining a small molecule in a region

Mark Abraham mark.j.abraham at gmail.com
Tue Jun 18 12:58:12 CEST 2019


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On Tue, 18 Jun 2019 at 12:45, ehsan shahini <ehsan.shahiny at gmail.com> wrote:

> Dear all,
> For the study of adsorption properties of a small molecule on a substrate
> (such as graphene), I would like to constrain the spatial mobility of the
> small molecule into a small cylindrical (or cubic) region so it can only
> move inside the region. A schematic image of my problem is attached. The
> entire simulation box is filled with an explicit water model and PBC in
> XYZ.
> How can I define this region in GROMACS?
> I was wondering if introducing a condition in the source code of mdrun
> could make it possible. That said, if any atom of the small molecule
> crosses the defined region then we get back a step and start the
> calculation for this step again. Is it possible?
> Kind regards,
> Ehsan.
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