GROMOS53a6 Gromacs by XYZ

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Lipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)
Pubchem CID:26197
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
dmpc.itp b68431f485caf2b4e7333e658bc1e757d52b21a3
lipids_vdw.itp 03dc690fd3d2858ae49e46037d1cde2a3cecdd9a
PDB structure
Bilayer structure
dmpc128_water.pdb df958f0e81c8a7fbaa88246d2848c9d559153eb9