I ran a simulation of a protein in water for 100ns, but no .gro file was outputted after the simulation ran (I am trying to see the structure using VMD). Can I convert a different file that was outputted (.xtc, .tpr, .log, .edr or .cpt) to a .gro file?
Are you sure the run completed? The output
.gro file is only the last snapshot. You can obtain the same snapshot with
gmx trjconv -f *.xtc -dump X, where X is the time (ps) of the last frame.
Thank you for your help. My simulation hadn’t finished properly.