Not sure how to convert a Gromacs trajectory file to Desmond trajectory file.

[mdbiology]

Hello, I want to convert an (xtc) trajectory file from Gromacs to Desmond file (cms).

How do I do this? Because in the manual, it says to input .gro and .top file but I already have finished the simulation in gromacs - but want to view it in the Desmond software.

Thank you!

[mrshirts]

You don't need intermol for this. There are a number of converters for structure files alone. Easiest thing would probably be to use gromacs trajconv to convert the .xtc file into a set of .pdb, and then Maestro should be able to read it. Software like OpenBabel also has more functionality, as does VMD (which can read .xtc). Intermol is for converting the instructions to run a simulation, not the trajectories.

[mdbiology]

Oh I see! Thank you so much for letting me know.