[gmx-users] computing electric field for triclinic system
mariiasavenko at gmail.com
Tue Dec 19 17:53:53 CET 2017
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.
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