Dear Dr Axel,
However, as is there a command “compute msd”, for translational diffusivity calculations, if there exists, some similar command (I hope there is some command in
you have not been paying attention to what I wrote. compute msd works on atoms. but since those are point particles, translation is well defined but rotation does not exist (angular momentum is infinity).
the msd of (a group of) molecules is simply the average over the individual atoms, since compute msd works on atoms, there is no conflict.
but if you want to analyse the rotation of molecules, that becomes a whole different procedure and data flow. first you have to define which are the constituent atoms (which can be done via molecule IDs), then you have to group them into something that you work on, e.g. into chunks via compute chunk/atom, then you need to compute orientation (which also requires defining a consistent direction within each molecule/chunk by determining the moments of inertia), then you need to access this data, i.e. you need a per-chunk compute to compute the orientation and then the angular velocity and then the corresponding auto-correlation or mean squared rotational displacement, and only then can you compute your rotational self-diffusion value. So to say, if there is a compute msd there could easily be a similar compute for rotational diffusion is arguing with semantics instead of science.
GROMACS, as I see the literature for estimation of “Rotational Mean Square Displacement” <phi(t)^2>), please let me know. People have of course calculated “Rotational Mean Square Displacement” < phi(t)^2> using LAMMPS, so I think there may be something like this in LAMMPS too.
as I already mentioned, anything that is provided with LAMMPS is documented. if you don’t see anything in the manual, it is not there. full stop.
now, if you want to use gromacs tools for post-processing, that is quite possible. you can generate a minimal gromacs topology from a LAMMPS data file using the VMD TopoTools plugin. that functionality was conceived many years ago with the specific intent of creating a topology (and through it a .tpr file) that is just enough for post-processing with gromacs.
Ref-“Molecular Dynamics Simulations of the Rotational and Translational Diffusion of a Janus Rod-Shaped Nanoparticle” appeared in Phys.Chem.B 2017, 121, 7133−7139 by Ali Kharazmi† and Nikolai V. Priezjev.
what you describe is something that most people I know do in post-processing.