Hello, I'm running some MD where I need to save frames _very_ frequently. Using DCDReporter(), it seems that file writing is the performance bottleneck in my case, which isn't ideal. Do you have any general tips on how I could speed this up? I can't speed up my cluster's file system, but maybe there...

If I use PDBFile.writeFile() to save a result of a simulation with PBC, can I use that file as an input for a subsequent simulation with the same PBC? I've been using the context.getState(...).getPositions() method to get coordinates. If I turn on the enforcePeriodicBox option in getState(), the str...

It would be nice to be able to monitor energy minimization with StateDataReporter(). I haven't been able to make it work. Is there no link between simulation.minimizeEnergy() and simulation.reporters?

Actually never mind just saw the documentation re Langevin integrator

Thank you! Was worried barostat wasn't supported for AMOEBA. One more q: John Chodera wrote in a old chat "Note that there can be issues when using finite-timestep MD without Metropolization together with a Monte Carlo barostat. The MC samples from the exact Boltzmann distribution, while the MD samp...

I read somewhere that this is a MacOS problem has something to do with permissions, hard to fix (https://stackoverflow.com/questions/223 ... ing-termin).

Hi everyone,

I'm very interested in using the AMOEBA FF. I need to equilibrate NPT and NVT before production run. However I saw in OpenMM documentation that "The virial is not calculated for any force." Can you do NPT in OpenMM with AMOEBA?

Thanks!