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- W2912072099 abstract "The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system. Typically, these are bond vibrations between hydrogen atoms and their parent heavy atoms, which require a 1-fs time step to ensure stability of the simulation. Imposing constraints on hydrogen-parent-atom distances permits a 2 to 3-fs time step, but angle vibrations prevent any further increase. An increasingly popular solution is to increase the mass of the hydrogen atoms to ∼3 amu and decrease the mass of the parent atom by an equivalent amount. This approach, known as hydrogen mass repartitioning (HMR), permits time steps up to 4 fs with reasonable simulation stability. While HMR has been applied in many published studies to date, it has not been extensively tested for membrane systems. Here, we compare the results of simulations of a variety of membranes and membrane-protein systems run using a 2-fs time step and a 4-fs time step with HMR. For pure membrane systems, we find practically no difference in structural properties, such as area-per-lipid and order parameters, and very little difference in kinetic properties such as the diffusion constant. Conductance through a porin in an applied field, partitioning of a small peptide, hydrogen-bond dynamics, and membrane mixing also show very little dependence on HMR and the time step. We also tested a shorter, 9-Å cutoff (vs. the standard CHARMM cutoff of 12 Å), finding significant deviations in almost all properties tested. We conclude that HMR is a valid approach for membrane systems but a 9-A cutoff is often not." @default.
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- W2912072099 date "2019-02-01" @default.
- W2912072099 modified "2023-10-16" @default.
- W2912072099 title "On the Validity of Hydrogen Mass Repartitioning for CHARMM36 Membrane Systems in NAMD" @default.
- W2912072099 doi "https://doi.org/10.1016/j.bpj.2018.11.782" @default.
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