Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations

Abstract

Molecular dynamics (MD) simulations have become an indispensable tool to investigate phase separation in model membrane systems. In particular, simulations based on coarse-grained (CG) models have found widespread use due to their increased computational efficiency, allowing for simulations of multicomponent lipid bilayers undergoing phase separation into liquid-ordered and liquid-disordered domains. Here, we show that a significant temperature difference between molecule types can artificially arise in CG MD membrane simulations with the standard Martini simulation parameters in GROMACS. In particular, the linear constraint solver (LINCS) algorithm does not converge with its default settings, resulting in serious temperature differences between molecules in a time step-dependent manner. We demonstrate that the underlying reason for this behavior is the presence of highly constrained moieties, such as cholesterol. Their presence can critically impact numerous structural and dynamic membrane properties obtained from such simulations. Furthermore, any preference of these molecules toward a certain membrane phase can lead to spatial temperature gradients, which can amplify the degree of phase separation or even induce it in compositions that would otherwise mix well. We systematically investigated the effect of the integration time step and LINCS settings on membrane properties. Our data show that for cholesterol-containing membranes, a time step of 20 fs should be combined with at least = 2 and = 12, while using a time step of 30 fs requires at least = 3 and = 12 to bring the temperature differences to a level where they do not perturb central membrane properties. Moreover, we show that in cases where stricter LINCS settings are computationally too demanding, coupling the lipids in multiple groups to the temperature bath offers a practical workaround to the problem, although the validity of this approach should be further verified. Finally, we show that similar temperature gradients can also emerge in atomistic simulations using the CHARMM force field in combination with settings that allow for a 5 fs integration step.

Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion

“…Hydrodynamics dictates that the effective viscosity in a single phase should be the same for all lipid types [23]. Here, the ratio of diffusion for DLiPC and DPPC lipids was closer to 0.5, which matched the ratio of diffusion coefficients in Martini simulations of planar phase separating systems [40]. This finding is in agreement with the observation that the lipid phases propagated along the flat membrane and spanned the simulation box (Fig.…”

Small ionic radii limit time step in Martini 3 molecular dynamics simulations

“…Another known issue that limits the time step in three-component phase separating systems is the presence of insufficiently converged constraints. 41 We plan to address this problem in a future publication.…”

LipIDens: Simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

“…mdp files for use with GROMACS) are automatically provided in the pipeline but users may wish to supply alternatives. The default linear constraint solver (LINCS) parameters () are used in mdp files unless MARTINI-2.2 cholesterol with virtual sites 3 is included in the bilayer, whereby and are used instead, in line with recent findings 4 .…”

“…Molecular dynamics simulation parameter files are automatically provided in the pipeline. The default linear constraint solver (LINCS) 49 parameters (lincs_order=4, lincs_iter=1) are used in GROMACS mdp files unless MARTINI-2.2 cholesterol with virtual sites 50 is included in the bilayer, in which case lincs_order=12 and lincs_iter=2 are used instead, in line with recent findings 51 48 ; and propKa (https://github.com/jensengroup/propka) 53 may be required.…”