Effects of the mass change on molecular motions

User discussions
1

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.

2

D2O moves slower than H2O, not faster.

The masses do not come into the force calculation. The only way masses affect MD is that the acceleration of atoms is inversely proportional to the mass (and the kinetic energy is affected, but that only has an indirect effects).