[gmx-users] computing electric field for triclinic system

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 22 11:31:58 CET 2017


You want to compute and plot the potential at particular points in space?
Why is periodicity a concern?


On Wed, Dec 20, 2017, 3:54 AM Mariia Savenko <mariiasavenko at gmail.com>

> Dear all,
> I have system in triclinic box. I'd like to plot a potential map on XY axes
> for a given Z in triclinic box, i.e. For a fixed value of Z I want to have
> plot of values in this plane.
> My system is a periodic "planar" molecule. Scripts using variations of the
> Ewald summation are mainly intended for orthogonal boxes. I concluded that
> only script which exists for my purpose is the one used internally by
> Gromacs. I know that Gromacs converts any triclinic box to a rectangular
> one. To ensure periodicity Gromacs uses shifted images of the unit cell
> along the triclinic axis. I'd like to understand how the PME algorithm of
> Gromacs manages with this issue and if anyone has been doing that.
> Sincerely,
> Mariia
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