Andrea Rizzi

It looks like `conda-forge` provides HDF5 libraries compiled with MPI enabled as of Nov 2018 (conda-forge/hdf5-feedstock#51) so netcdf with parallel writing should be a feasible option if we decide to...

Ah! But conda-forge/libnetcdf is built only with `openmpi`, not `mpich` (and only since a couple of months ago) so it may be more complicated than I thought (conda-forge/netcdf4-feedstock#43). It might...

I took a look at what it will take to get an mpich variant built on the netcdf4 feedstock. It looks quite easy, and they seem open to external contributions...

> Can we discuss Monday? Sure! I just found out that parallel netcdf doesn't support neither compression nor chunk caching. This might be ok for the checkpoint trajectory, but it...

Me and @jaimergp had a brief chat. If there are no objections, the current plan is to have @jaimergp implement splitting the solute-only trajectory on multiple `xtc` file, and re-evaluate...

For the records, we are going to merge #434, which split solute-only trajectories from the main netcdf and saves them into separate `xtc` file, in a `parallel-writing` branch. Right now...

@jaimergp implemented the parallel XTC files and we have now merged them in a separate feature branch (`parallel-writing`). If I remember correctly, it's not in master right now because we...

Hi @chemlove . I'm not sure I understand your requirements exactly, but I suggest you look at the `CustomCVForce` in OpenMM (http://docs.openmm.org/latest/api-python/generated/simtk.openmm.openmm.CustomCVForce.html#simtk.openmm.openmm.CustomCVForce). Currently, the simulation doesn't store the CVs, but...

Also, moving away from the unsupported `nose` and switching to `pytest` is my best bet to get rid of the annoying and persistent segfaults on macOS.

Thank you! I think this is ready to be merged. Can you just update the `releasehistory.rst` in `docs/` before?