While mapping atoms with different masses is reasonable in many cases, it can be handy to have an option for not doing so. The reason, is that mass changes are not supported in GROMACS on GPU at the moment. While it can change in the future, for now those changes are only possible with update step on CPU, which blocks efficient running in the cloud. I gave it a try locally, by postprocessing created pairs to remove atoms with different masses and hydrogens attached to those from the mapping. I did not observe any significant performance degradation. Since I was not really interested in the score, I was not updating it.
The plan for the change can be:
- Add a flag
- Add a check for mapped atoms to have similar mass
- Exclude hydrogens from mapping, if they are accidentally mapped (e.g. CH3 -> NH3+)
- Update score
@vgapsys If the plan sounds reasonable, I can start working on it
While mapping atoms with different masses is reasonable in many cases, it can be handy to have an option for not doing so. The reason, is that mass changes are not supported in GROMACS on GPU at the moment. While it can change in the future, for now those changes are only possible with update step on CPU, which blocks efficient running in the cloud. I gave it a try locally, by postprocessing created pairs to remove atoms with different masses and hydrogens attached to those from the mapping. I did not observe any significant performance degradation. Since I was not really interested in the score, I was not updating it.
The plan for the change can be:
@vgapsys If the plan sounds reasonable, I can start working on it