An efficient method for extracting volumetric data from simulations is developed. The method is illustrated using a recent atomic-level molecular dynamics simulation of L(α) phase 1,2-dipalmitoyl-sn-glycero-3- phosphocholine bilayer. Results from this simulation are obtained for the volumes of water (VW), lipid (V(L)), chain methylenes (V2), chain terminal methyls (V3), and lipid headgroups (V(H)), including separate volumes for carboxyl (V(COO)), glyceryl (V(gl)), phosphoryl (V(PO4)), and choline (V(chol)) groups. The method assumes only that each group has the same average volume regardless of its location in the bilayer, and this assumption is then tested with the current simulation. The volumes obtained agree well with the values VW and V(L) that have been obtained directly from experiment, as well as with the volumes V(H), V2, and V3 that require certain assumptions in addition to the experimental data. This method should help to support and refine some assumptions that are necessary when interpreting experimental data.
Petrache, H. I., Feller, S. E., & Nagle, J. F. (1997). Determination of component volumes of lipid bilayers from simulations. Biophysical Journal, 72(5), 2237–2242. https://doi.org/10.1016/S0006-3495(97)78867-2