GROMACS version: 2024.1
GROMACS modification: No
Greetings, everyone!
I have a perhaps less practical question that I am hoping someone can help me with. I am having trouble understanding the energy calculations (and recalculations) that take place during mdrun when simulating two or more molecules.
As per recommendations I have read in this forum and in various tutorials, when performing mdrun for a protein and a ligand, I first used a molecular parameters file without energy groups defined in the output control to be able to generate the main trajectory using the computer’s GPU, and then used the -rerun flag on this trajectory but using a .tpr file generated from a .mdp with multiple energy groups and ran that on the CPU. However, I am having trouble understanding how this works in basic terms.
Is the only difference between these two commands that GROMACS doesn’t write out the separate energies for separate groups when running the original simulation? I have to imagine the same “bulk” energies are being calculated in both cases, since the energies dictate each following step, so how is that energy calculation different in these two instances when it seems necessary that there aren’t any numerical changes between them as not to change the entire trajectory that was calculated the first time around?
Any elucidation regarding this topic will be much appreciated.