Michael Quevillon

Hmmm, I don't think that SSAGES is able to handle a dedecahedral box properly. Our current implementation unwraps PBCs assuming you have a rectangular box. There could definitely be issues...

Ideally, SSAGES would have printed a warning or error message for you, instead of having to figure it out on your own. I'm definitely adding this to the developers' to-do...

Actually, from diving further into the GROMACS documentation, it should convert dodecahedral and octahedral boxes into triclinic cells, internally. This would mean that SSAGES is actually unwrapping correctly, regardless of...

As mentioned previously, GROMACS converts essentially all box geometry to triclinic cells to create the box matrix (`H`). We have not done extensive testing with triclinic cells (or dodecagons or...

You are correct that multiple MPI processes are trying to read/write at the same time, which corrupts the dumpfiles. Because of this and a few other quirks, the current implementation...

SSAGES v0.9.3 will now throw an error if the user tries to use more than 1 MPI process per walker. While we would like to get full MPI support for...

Thank you for your interest in our project! Unfortunately, our implementation of FTS does not yet natively calculate the free energy along the path. In our examples, we have typically...

Unfortunately, the current FFS implementation is set up for 1 MPI process per walker. This is a definite shortcoming of this method at this time, and we will most likely...

The `"output_frequency"` parameter sets how often a histogram is output from SSAGES. While we do not necessarily have a feature to determine convergence automatically, it should be relatively easy to...

A simple way of performing this would be to run successive 50 ns simulations. Make sure that the `restart: True` flag is turned on (in JSON) to continue the ABF...