Sorry for these basic questions.
Last time Dr. Lemkul said “energygrps should NOT be used during an MD simulation and should be treated as an analysis method.”
But if energygrps e.g. “energygrps = non-Water” is already included in a normal md.mdp file(not ie.mdp), can this affect normal MD simulation results? such as free energy results?
In addition, “compressed-x-grps = non-Water” would remove all water in xtc file, can this affect MD simulation results? such as free energy results?
I guess all water are still kept in simulation process.