peastman wrote: ↑

Tue May 11, 2021 12:33 pm

No, it's built into the barostat algorithm. Sorry!

No worries. Thanks for confirming it. I can try to unwrap the trajectories in post-analyses, but it would be nice if I can obtain the unwrapped trajectories from OpenMM directly.

Thanks a lot for the prompt response too!

If you're running a constant pressure simulation, the barostat will wrap the molecules into a single periodic box every time it rescales the box. Thanks a lot for the reply. My simulation is indeed NPT. Is there an option to turn off the wrapping without turning off PBC altogether in barostat, by a...

Hi All, I am trying to run a simulation with periodic boundary conditions. I have nonbonded forces in the system with a cutoff of 10 angstroms. I would like to obtain unwrapped positions of the atoms for some downstream analyses, but I found that the positions obtained from my simulation seem to be ...