Hi! I'm exploring the possibility of using OpenMM and AMOEBA to calculate vibrational spectra of water. I was wondering how OpenMM can be used to extract the dipole and polarizability of atoms/molecules of interest from an AMOEBA simulation. I don't know if this is even possible but I thought I woul...

Update: velocities are included if velocities=True is specified when initializing the reporter, but not if reporter.velocities = True is set later.

I tried the advice above with hdf5 reporter and the even though i said velocities = True, the hdf5 file doesn't have velocities, only coordinates. Is it possible that mdtrajreporters.hdf5reporter just hasn't implemented velocity writing yet, despite the documentation? It would be really great if Ope...

It seems the MDtraj netcdf reporter can't write velocities. Is the MDTraj/OpenMM team planning to add velocities to this tool soon?

An update: I tried "velocities" and while it successfully sets the parameter to True (checked vars()), velocities are still not written. Is it possible that the MDTraj DCDReporter hasn't implemented velocity writing yet and the documentation is ahead of the code? Should I just use DCDReporter from t...

Oh ok. Thank you. I thought there was something odd about the naming!

Hi, here I am again. I am trying to use MDTraj's dcdreporter to write both coordinates and velocities to a trajectory. I am using this tool: https://mdtraj.org/1.9.3/api/generated/mdtraj.reporters.DCDReporter.html#:~:text=Either%20an%20open%20DCDTrajectoryFile%20object,to%20save%20the%20trajectory%2...

Oh ok I see. I will set it to 1 then and just make the timestep 0.5 fs. I thought it wanted the time not the number of steps. Thank you!

I need to run a short flexible water trajectory with a timestep of 0.5 fs and save configurations for each timestep. I am getting this error traceback (below). Something about saving every 0.5 fs is bothering OpenMM. Is there a way to get around this? I have no problems if the saving frequency is 1....

Oh ok, I understand. It seems like AMOEBA is a better choice for protein containing systems with flexible water, but AMBER + flexible water may be useful for trial runs, etc.