Hi all,

I am a newbie in the field of classical MD calculations for biomolecules, and I am running a few calculations for studying protein-ligand interactions using the GROMOS force field in GROMACS, following the protocols in Justin Lemkul's (great) tutorials.

I am running some test calculations with a time step of 4 fs (double the value used in the tutorials) leaving the rest of the parameters in the .mdp files unchanged. It turns out that temperature and total, potential and kinetic energies seem to be pretty well-conserved with that time step up to 2 ns in the production MD run (the total simulation time is 50 ns, which should be ready soon).

So, I would appreciate if more experienced users could tell me: if by the end of my test calculation a time step of 4 fs does indeed conserve total, kinetic and potential energies, would there be any spurious effects on the interactions between the protein and the ligands?

Best regards,

Marcos