Secondary structure assignment via DSSP as native gromacs code
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:
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.