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Using nMOLDYN in the Python 3 era

nMOLDYN has been developed over many years. It was originally written in Python version 2.2, based on libraries that went back to the early days of the scientific Python ecosystem in the 1990s. Porting these libraries to Python 3 would have represented a major effort for which we could not gather the required resources. After Python 2 was sunset in 2020, it became increasingly difficult to install and use on modern operating systems. While in 2022 it is still possible to follow the original nMOLDYN installation instructions (see README), starting from source code, it is probable that this will become more and more cumbersome.

We therefore recommended installing nMOLDYN via the Guix package manager, which allows using conflicting versions of libraries in parallel and has excellent support for reproducible computations. A special Guix channel provides much of the Python 2 ecosystem and makes it easy to install on any modern Linux system. We have added nMOLDYN to this collection.

To install nMOLDYN via Guix, you must be running the GNU/Linux operating system. The steps are:

  1. Install Guix as described in its manual
  2. Create the file ~/.config/guix/channels.scm containing the following lines:
(use-modules (guix ci))

(list (channel
        (name 'nmoldyn)
        (url "https://github.com/khinsen/guix-past")
        (branch "nmoldyn"))
      (channel-with-substitutes-available
          %default-guix-channel
          "https://ci.guix.gnu.org"))
  1. Run guix pull to update Guix' package definitions.
  2. Run guix install nmoldyn.

You can then run nMOLDYNStart.py.