期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 15, 期 8, 页码 4673-4686出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.9b00160
关键词
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资金
- National Science Foundation [MCB-1452464]
- National Institutes of Health [R01-GM123169]
- Research Grants Council [14323816]
- Chinese University of Hong Kong
- National Institute on Drug Abuse [RO1-DA003934]
- NSF [OCI-1053575]
The time step of atomistic molecular dynamics (MD) simulations is determined by the fastest motions in the system and is typically limited to 2 fs. An increasingly popular approach is to increase the mass of the hydrogen atoms to similar 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-containing 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 almost no difference in structural properties, such as area-per-lipid, electron density profiles, and order parameters, although there are differences 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 show very little dependence on HMR and the time step. We also tested a 9 angstrom cutoff as compared to the standard CHARMM cutoff of 12 angstrom, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 angstrom cutoff is not.
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