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Biophys J, May 2002, p. 2317-2325, Vol. 82, No. 5

Simulations of Membranes and Other Interfacial Systems Using P21 and Pc Periodic Boundary Conditions

Elizabeth A. Dolan,* Richard M. Venable,dagger Richard W. Pastor,dagger and Bernard R. Brooks*

 *Laboratory of Biophysical Chemistry, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892; and  dagger Laboratory of Biophysics, Center for Biologics Evaluation and Research, Food and Drug Administration, Rockville, Maryland 20854 USA

We demonstrate the ease and utility of simulating heterogeneous interfacial systems with P21 and Pc periodic boundary conditions which allow, for example, lipids in a membrane to switch leaflets. In preliminary tests, P21 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. P21 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 P21 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.

Biophys J, May 2002, p. 2317-2325, Vol. 82, No. 5
© 2002 by the Biophysical Society   0006-3495/02/05/2317/09  $2.00


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