Artifacts in dynamical simulations of coarse-grained model lipid bilayers

Jakobsen, Ask F.; Mouritsen, Ole G.; Besold, G.

doi:10.1063/1.1900725

Cited by 60 publications

(61 citation statements)

References 56 publications

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“…The time step used for propagation was 0.0025 ͑and 0.01 for the long time bending modulus calculations͒. While the small time step is important to avoid simulation artifacts in the calculation of the pressure tensor, 33 we found that the resulting curves were virtually the same using either 0.0025 or 0.01 , in which data were collected for over 1500 . Periodic boundary conditions were applied, and interactions followed the minimum-image convention as the model incorporates no long-range forces.…”

Section: A Simulation Protocolmentioning

confidence: 74%

“…Perhaps the disagreement arises from known simulation artifacts in the calculation of the pressure tensor for "soft" mesoscale models, or possibly due to the integration error that accumulates from an ill-defined time step. 33 Efficient DPD simulations have reproduced a qualitatively correct stress profile; in a review of membrane models, Venturoli et al 17 reproduce a stress profile that has the same features as the all-atom simulation. Finally, detailed explicit solvent coarse-grained simulations, such as the MARTINI forcefield 19 and a LJ/GayBerne lipid model, 60 nicely reproduce all-atom stress profiles.…”

Section: Discussionmentioning

confidence: 99%

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An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

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Section: A Simulation Protocolmentioning

confidence: 74%

Section: Discussionmentioning

confidence: 99%

An implicit solvent coarse-grained lipid model with correct stress profile

Sodt

Head‐Gordon

2010

The Journal of Chemical Physics

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“…Specializing this equation for a bilayer, we find that dP N /dz = 0, and therefore the normal stress profile should be constant. This physical requirement has been invoked to assess the quality of simulation protocols 49 or stress calculation methods. 50 Its violation in atomistic simulations of lipid bilayers 26,29,30,33 has sparkled some controversy about the role of constraints, as discussed in the previous section.…”

Section: Stress In Lipid Bilayersmentioning

confidence: 99%

Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations

Vanegas

Torres-Sánchez

Arroyo

2014

J. Chem. Theory Comput.

141

156

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Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions.However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations, e.g. non-constant normal stress profiles along an isotropic bilayer in equilibrium, is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of * To whom correspondence should be addressed † Universitat Politècnica de Catalunya-BarcelonaTech ‡ Contributed equally to this work 1 dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations.

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“…To illustrate the application to complex fluids, simulations of the same lipid bilayer model studied previously [26,30,31] have been carried out with the new thermostat. Here, the solvent water is represented as before, and each lipid molecule has the form of a 7-bead chain HT 6 in which α-repulsion parameters between hydrophilic "head" beads (H), hydrophobic "tail" beads (T), and "water" beads (W) are chosen to produce the desired behaviour [30].…”

Section: Resultsmentioning

confidence: 99%