GROMACS version: 2022-rc1
Hi, I am a quite new user of Gromacs, and I have a basic question related to the integrator for Free Energy Perturbation calculation as written in the tutorial of Justin Lemkul. In the tutorial, the integrator is set as stochastic dynamic. Nevertheless, I want to know what happened if I run my FEP with Leap Frog. So I run the vdW-coupling process applying Gauss Legendre Quadrature nodes, I got a note from Gromacs:
“NOTE 1 [file /home3/hij09373/fep/2_ribo_water/MDP_vdw/nvt_0.mdp, line 81]:
For proper sampling of the (nearly) decoupled state, stochastic dynamics
should be used”
So I assume, that Leap Frog is not preferable in this case, at least for nearly decoupled states. Due to my background in quantum chemistry and not MD, I am not quite sure what is the impact of “decoupled state” with either LF oder Langevin. While I do might understand the difference between the integrators, I might miss some crucial points in these detailed aspects in FEP. May be somebody has already answered this, but at the moment I could not find this. Can somebody explain this in short or even give me some elaborate literatures?