Coarse Grained Force Field

Introduction

A coarse grained force field relies on less detail than a traditional atomistic (all-atom or united-atom) force field.  Functional groups are represented by coarse particles rather than individual atoms.

Time Step

The reasoning of a coarse grained force field is a bit different than for an all-atom force field. In an all-atom force field you assume the free energy surface the force field describes is actually exact and the smaller the time step, the more accurate you are. You then try to increase the time step to be able to sample bit more and increase your statistics.

In the case of a coarse grained force field, and especially for the MARTINI one, you use an approximated potential energy surface of the all-atom force field (with a strong smoothing of the surface) but you should reproduce all-atom and experimental observables. Given the coarse grained force field (set of parameters), and thus the potential energy surface of the system, the way you are going to explore this particular surface is actually dependent upon many parameters, and time step is one of them. A reduction of the time step would favor the states of the system with the lower potential energy. This is equivalent to playing with the temperature. This is also true for the cutoff.  Do not modify the cutoff; it is part of the force field. Increasing the cutoff will not make your run more accurate, but on the contrary, will alter the balance of the different terms.

In summary, the time step determines the balance between enthalpy and entropy. The smaller the time step, the smaller the entropy. The force field as been parameterized to be valid in the range 0.02-0.04 ps.

The effect on the partitioning free energy of the beads is up to ~5% when going from 4 to 5 fs time step. This was reported in the MARTINI paper. Although the effect is small, it is present and it is better that users know and use the time step used for the parameterization in order to avoid altering the properties of the force field and thus the description of the system. Although the effect is marginal, we are dealing with multi-microsecond simulations and small differences could be observed.

It is important to keep in mind that the MARTINI model is a coarse grained approach and thus: "...considering the inherent approximative nature of the underlying CG potentials, this is not problematic per se as long as the time step used in simulations does not differ too much from the time step used for the parametrization." Quote from the MARTINI paper.