GROMOS53a6 Gromacs by XYZ

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Lipid 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine (POPC)
Pubchem CID:5497103
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy. Specifically, the solvation and the orientation of the dipole of the phosphocholine headgroup and of the ester carbonyls show that the structure of the primary hydration shell in the simulations closely matches experimental findings. This work highlights the need to reproduce a broad range of properties beyond the area per lipid, which is poorly defined experimentally, and to consider the effect of system size and sampling times well beyond those commonly used.

Based on Supplementary Information from JCTC


David Poger, Alan E. Mark, On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment, JCTC 6 (2010), 325–336, doi: 10.1021/ct900487a, [no pubmed id]
Primary Experimental


Version 1
popc.itp 6fb72fb80f51e7bba8a00c49a0b6baa70d5a6b7f
lipids_vdw.itp 03dc690fd3d2858ae49e46037d1cde2a3cecdd9a
PDB structure
Bilayer structure
popc128_water.pdb 024f2b8984a2a0a1a9fe84f19517ae44b6af467b