Chris Iacovella

The lammps data file should contain the bounds of the simulation cell (see: https://lammps.sandia.gov/doc/2001/data_format.html) I just submitted PR related to the simulation cell bounds not being set properly (things were...

I can see how moving recipes like "alkane" to a different repo would be good, but I agree with @mattwthompson that some basic recipes should be included, especially the more...

For the amorphous silica, I poked the surface using a regular grid (you can specify the probe size). I'll note that I first identified surface particles by doing a rough...

I think we should also add some text somewhere in our readme for foyer that says some variant of the following things: 1- if you are taking parameters from a...

This is a good idea. Until this change is put into place, I suggest all force field files should start with a comment that clearly states the expected units. We...

Good idea. As Andrew and I just discovered, forcefield size seems to play a significant role as the system size increases. As we've discussed before, we should have a "reduce"...

Check out Automated Topology Builder (and some of their associated papers linked on the website). They go into detail with regards to the different methods for chopping up the system...

The JCTC paper about ATB has a lot of good details: http://pubs.acs.org/doi/abs/10.1021/ct200196m As does their most recent paper on improving it (I don’t have access to the full journal, but...

This PR implements the logic in effectively the same way as the old code, which is on a per-record basis (i.e., a function operates on a single record name). The...

> This line will need to get changed @chrisiacovella https://github.com/choderalab/espaloma/pull/187/files#diff-ba5d22563299549a389183418fe5786b83275382be592bf1ed06fae673b7d086L23 Sorry about that! Good catch.