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. 2023 Nov 30;19(23):8919–8929. doi: 10.1021/acs.jctc.3c00777

Figure 1.

Figure 1

Large Martini POPC bilayer crumples in MD simulations with default simulation parameters, yet stays flat with frequent neighbor list updates. (A) Snapshots of the membrane (phosphate groups in gold) in MD simulation with default parameters. The Verlet-buffer-tolerance, which denotes the maximally allowed energy drift per particle between neighbor list updates due to missed nonbonded interactions, was set to VBT = 0.005 kJ·mol–1·ps–1; the outer cutoff was rl = 1.269 nm; the number of time steps between neighbor list updates was nstlist = 25; and dual pair list was enabled. (B) Snapshots in an MD simulation with neighbor list updates enforced at every time step (nstlist = 1). Snapshots are at time points 50, 150, 250, and 350 ns (left to right). Simulation boxes are indicated as blue lines, and box heights Lz are listed.