GROMACS

The GROMACS do_dssp analysis tool enables secondary structure analysis over a trajectory.

The tool, however depends on a call to the externally to be installed dssp tool, which is maintained here:

https://github.com/cmbi/xssp

User regularly complained about the challenge to get dssp set up correctly, and the main branch is currently broken from Ubuntu 18.04.
The current do_dssp implementation calls dssp and writes and parses back a dssp output file for every trajectory frame.

A GROMACS native dssp implementation will

• greatly facilitate use of secondary structure assignment for trajectories, because it ships "out of the box" * speed up the analysis too, because no writing and reading of temporary files is needed * is a requirement for driving simulations to secondary structure targets, with a secondary structure assignment that can run in simulation time

The current xssp suite that includes dssp has a boost license that should allow the modification of their code for our purposes, however, okay from the software maintainers is still pending.