PDF(Pubmed)
Abstract：
Consistent buckling distortions of a large membrane patch (200 × 200 Å) are observed during molecular dynamics (MD) simulations using the Monte-Carlo (MC) barostat in combination with a hard Lennard-Jones (LJ) cutoff. The buckling behavior is independent of both the simulation engine and the force field but requires the MC barostat-hard LJ cutoff combination. Similar simulations of a smaller patch (90 × 90 Å) do not show buckling, but do show a small, systematic reduction in the surface area accompanied by ~1 Å thickening suggestive of compression. We show that a mismatch in the way potentials and forces are handled in the dynamical equations versus the MC barostat results in a compressive load on the membrane. Moreover, a straightforward application of elasticity theory reveals that a minimal compression of the linear dimensions of the membrane, inversely proportional to the edge length, is required for buckling, explaining this differential behavior. We recommend always using LJ force or potential-switching when the MC barostat is employed to avoid undesirable membrane deformations.
摘要：
在分子动力学（MD）模拟中，使用蒙特卡洛（MC）压力调节器结合硬的伦纳德-琼斯（LJ）截止，观察到较大的膜片（200×200µ）的一致屈曲变形。屈曲行为与模拟引擎和力场无关，但需要MC气压调节器-硬LJ截止组合。较小的贴片(90×90)的类似模拟没有显示屈曲，但确实显示了一个小的，表面积的系统减少，伴随着约1µ增厚，提示压缩。我们表明，在动力学方程与MC气压调节器中处理电势和力的方式不匹配会导致膜上的压缩载荷。此外，弹性理论的直接应用揭示了膜的线性尺寸的最小压缩，与边缘长度成反比，需要屈曲，解释这种差异行为。当使用MC稳压器时，我们建议始终使用LJ力或电位切换，以避免不良的膜变形。
