GROMACS modification: Yes/No
I wanted to test how the different isotope makes the difference. So to test this in extreme case, I scaled my system mass of protein by 1 million to see the effect. Surprisingly, it changed the pressure of the whole system. The pressure of the system is changed so much so that pbc block is no longer retain the original shape. I personally don’t think the protein mass will not change the system pressure since it is not moving. Is there any place in program that assume mass of C is 12 even if user specify different mass? Am I conceptually missing some concept here? Thank you very much.