Accelerating Membrane Simulations with Hydrogen Mass Repartitioning
- UNCG Author/Contributor (non-UNCG co-authors, if there are any, appear on document)
- Patricia H. Reggio, Professor and Department Head (Creator)
- Institution
- The University of North Carolina at Greensboro (UNCG )
- Web Site: http://library.uncg.edu/
Abstract: 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 ~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 Å cutoff as compared to the standard CHARMM cutoff of 12 Å, finding significant deviations in many properties tested. We conclude that HMR is a valid approach for membrane systems, but a 9 Å cutoff is not.
Accelerating Membrane Simulations with Hydrogen Mass Repartitioning
PDF (Portable Document Format)
762 KB
Created on 3/30/2020
Views: 1222
Additional Information
- Publication
- Journal of Chemical Theory and Computation 2019, 15, 8, 4673-4686
- Language: English
- Date: 2019
- Keywords
- lipids, molecular dynamics, diffusion membranes