OpenMM
- Is OpenMM the only way to run simulations?
- Absolutely not.
- Are there multiple integrator types and barostats? Why did you choose the ones you did?
- Probably.
- Can I use a force field family other than AMBER with OpenMM?
- FIXME
- Can I only use the prmtop and inpcrd file formats as inputs?
- FIXME
- Does this work on both CPUs and GPUs?
- Yep.
How do I “baby the simulations”? ; FIXME
- Does MPI for Python exist?
- Boy howdy does it. You can read more in the MPI for Python documentation.
- What’s this 0.999 nanosecond thing about?
- FIXME
- If I were going to start doing this full time, what quirks or problem areas should I be aware of?
- FIXME
MDAnalysis
- Are there other ways to analyze trajectories?
- I assure you,
cpptrajexists.