[gmx-users] computing electric field for triclinic system

[Mariia Savenko]

Yes, I'd like to compute potential in particular plane in my box. What I
find to be a problem, that computing PME in triclinic box is not so
trivial. If I understand rightly FFT requires orthonormal space as "input".

22 груд. 2017 р. 11:32 дп "Mark Abraham" <mark.j.abraham at gmail.com> пише:

> Hi,
>
> You want to compute and plot the potential at particular points in space?
> Why is periodicity a concern?
>
> Mark
>
> On Wed, Dec 20, 2017, 3:54 AM Mariia Savenko <mariiasavenko at gmail.com>
> wrote:
>
> > 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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