GROMACS version: 2018.3
GROMACS modification: No
I carried out two MD simulations on protonated and perdeuterated molecules in the same solvent (water). Here, I changed the mass of all the H atoms in the molecules to 2 instead of 1 in the topology file (.top and .tpr).
The results showed that the perdeuterated molecule moves faster (,which is supported by experiments).
My question is:
By changing the mass, what terms in energy and force calculations in GROMACS are affected (other than kinetic energy)? The Lenard-Jones potentials and electrostatic interactions should be unchanged by mass increase.
I wonder why the heavier molecules move faster than their lighter counterpart…
Thank you in advance.