Sofia Bariami

hi Lester, yes, can you delete the `feature_virtual-sites` branch please? I left it to delete = it myself later on, but I don't need it anymore

Hi Julien, Yes, I managed to do it. The problem is that I am now getting a Segmentation Fault every time I am trying to calculate energies of molecules with...

The problem was that I had also written code for openmmmdintegrator.cpp, that wasn't needed. After I commended it out of the file, the implementation of the VS worked. The energies...

Thank you @chryswoods and @jmichel80 for the suggestions. Here are some thoughts about the implementation: First of all, if we set the virtual site as a zero-mass atom, does this...

@lohedges , sorry I didn't see the notification earlier, good points! @jmichel80 yes, no problem, I will add a unit test. So far we have only converted molecules in vacuum,...

I wrote a unit test that generates amber files, calculates the energies using the amber and qube files separately and then uses `assert_almost_equal()` to compare the energies. You can find...