Viewing lipid POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

modified CHARMM27 POPC parameters The IC (internal coordinates) rows in the POPC residue are incorrect. Usually this is not a problem but if one is adding hydrogens and getting psfgen to guess their positions then the errors in the IC rows will cause the hydrogens to be added in [...] [read more]

Parameters taken from lipid.itp found at: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies POPC bilayer self-assembled using CG then converted to atomistic by CG2AT. Atomistic bilayer equilibrated though 10 ns of MD.

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 [...] [read more]

POPC atomistic parameters developed by Peter Tieleman.

The lipid.itp comes from P. Tieleman's lab webpage.
The ffgmx*.* are the gromos parameters (come with Gromacs package). Both of these files are the versions available in 2007.

OPLS-UA lipids consistent with the OPLS-AA force field.

Please cite: J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813

POPC GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.

If you use these parameters please read and cite:

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. Thomas J. Piggot, Ángel [...] [read more]

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GAFFlipid parameter files for simulation of POPC using AMBER. Also included are PDB files of 72, 288 and 2x288 POPC bilayers.

 

To unzip: tar -xvzf POPC.tgz

Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop [...] [read more]