Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.
We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P2(1) and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P2(1) was shown to yield equivalent results to P1 in simulations of bulk water, a water/vacuum interface, and pure DPPC bilayers with an equal number of lipids per leaflet; equivalence of Pc and P1 was also demonstrated for the former two systems. P2(1) was further tested in simulations involving the spreading of an octane film on water, and equilibration of a DPPC bilayer from an initial condition containing different numbers of lipids in the two leaflets. Lastly, a simulation in P2(1) of a DOPC/melittin membrane showed significant passage of lipids to the melittin-containing leaflet from the initial distribution, and lends insight into the condensation of lipids by melittin.
Dolan
Elizabeth A
EA
Laboratory of Biophysical Chemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Venable
Richard M
RM
Pastor
Richard W
RW
Brooks
Bernard R
BR
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D001665:Binding Sites; D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry*; D008567:Membranes, Artificial; D008958:Models, Molecular; D008968:Molecular Conformation; D009795:Octanes / Q000737:chemistry; D010713:Phosphatidylcholines / Q000737:chemistry; D012984:Software; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
D008051:Lipid Bilayers; D008567:Membranes, Artificial; D009795:Octanes; D010713:Phosphatidylcholines; D014867:Water; D015060:1,2-Dipalmitoylphosphatidylcholine; C017251:1,2-oleoylphosphatidylcholine; C026728:octane