[gmx-users] Solvating dodecahedron

[Tsjerk Wassenaar]

Hi Justin,

> Note that the pseudo-sphere representation is for visualization
> purposes only; the triclinic cell should be the input for any simulation.

This not true. It doesn't matter which representation you use as
input. Molecules may be broken over PBC, but the topological
information is taken from the .tpr file anyway. Gromacs may spit out
broken molecules, and will swallow them just as well.

Groetjes,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands