Analyzing simulations run with OpenMM

OpenMM uses set up files from a bunch of different sources, so we can't give example command lines the way we do for the other packages. However, we can give a few general pointers

1. Read the other package-specific documents on this wiki.
2. If you built your simulation using GROMACS, consider running gmxdump2pdb.pl to generate a fake PSF file for use in analysis. This isn't mandatory, but PSF files have a lot of additional information (charge, mass, bonds) that are absent from GRO files, and LOOS can take advantage of that.
3. DEPRECATED If you built your simulation directly in OpenMM, you can use openmm2psf.py to generate a fake PSF, since OpenMM state files aren't particularly information-rich. openmm2psf.py must be run using the same environment you use to run OpenMM (it runs OpenMM behind the scenes). At some point, we may add it to LOOS proper, but for now it's a standalone beast. It does not produce a real PSF file, so don't try to use its output to drive NAMD.
4. A better way to get a good system file from the OpenMM build tools is to use parmed to make a PSF file. Something like this should work (credit to Mehtap Isik, @MehtapIsik):

import parmed as pmd

struct = pmd.openmm.load_topology(pmd.load_file('../openmm_outputs/equilibrated.pdb').topology,
                                  pmd.load_file('../openmm_outputs/system.xml'))
struct.save('system.psf', overwrite=True)