To convert Desmond molecular dynamics (MD) simulation trajectory files to a Gromacs-compatible format, the general workflow involves extracting the trajectory and topology/structure from Desmond outputs and converting them—typically with tools like VMD, MDTraj, or InterMol.

To convert Desmond MD trajectory (.dtr or .dcd) to GROMACS (.xtc/.trr), use VMD:

1. Open VMD, load your Desmond structure (.cms or .pdb).

2. Load the trajectory (.dtr folder or .dcd file).

3. Save as .trr via File > Save Coordinates.

4. (Optional) Convert .trr to .xtc in GROMACS: `gmx trjconv -f input.trr -s ref.gro -o output.xtc`.

Or use MDTraj in Python:

import mdtraj as md

traj = md.load('path/to/trajectory.dtr', top='your_structure.cms') # Or .dcd

traj.save('output.xtc') # Saves as GROMACS XTC

Ensure atom order matches. You’ll need a GROMACS topology (.top/.tpr) for analysis—try ACPYPE to convert .cms.

https://learn.schrodinger.com/public/python_api/2025-3/trajectories.html

You can perform a direct conversion using the dtr2xtc.py script. I do not recommend creating your topology file in Maestro. Maestro places “dummy” atoms and sometimes causes errors. It makes more sense to save the first frame of your trajectory in PDB format using Pymol or VMD.