search

openmm / openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)
http://openmm.org
Other
256 stars 81 forks source link

Saving trajectory without wrapping #304

Closed CheggQuery closed 1 year ago

CheggQuery commented 1 year ago

I am running a Brownian dynamics simulation (openmm.BrownianIntegrator(300 kelvin, 91/ps, 2 fs)) for a protein in the presence of ions. I want to calculate the dynamic properties like the translational diffusion coefficient. For calculating the dynamic properties we need unwrapped trajectories. Therefore, I used dcdreporters as simulation.reporters.append(app.DCDReporter('traj.dcd',2 fs,enforcePeriodicBox=False)).

However, after running 2 microseconds, there is only 45 angstrom translation in the center of mass of the protein. Is it enough to write only enforcePeriodicBox=False in the dcdreporter to turn off pbc wrapping?

mattwthompson commented 1 year ago

I see you've opened the same issue in OpenMM's issue tracker - that's where this should go, so I'm closing this duplicate.