Slipids/AMBER Gromacs by XYZ

The package viewer shows the meta data for the package and the available versions, i.e. the history of the parameters. Note that files can differ between versions, in which case the SHA1 checksum after the filename will differ. You can read and add comments for a particular version through the View discussion button on each version.

If you are the curator of a package (i.e. you added it) and you are logged in then you can also edit the package.

Lipid 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE)
Pubchem CID:5282290
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck

An all-atomistic force field (FF) for saturated PC lipids coined Stockholm lipids (Slipids). All parameters have been developed in a consistent and physical sound way. All the partial atomic charges have been recalculated at the B3LYP/cc-pVTZ level of theory by fitting the electrostatic potential. Lennard-Jones and torsional parameters were refitted from experimental data and high level ab-initio calculations, respectively. The remaining parameters are taken from C36.

The abilities of Slipids is proven in J. Phys. Chem. B, 2012, 116 (10), 3164-3179 (http://pubs.acs.org/doi/abs/10.1021/jp212503e, open access) and J. Chem. Theory Comput., 2012, DOI: 10.1021/ct300342n. A number of experimental properties such as area per lipid and thicknesses are reproduced. More importantly, X-ray and neutron scattering form factors and NMR order parameters are in excellent agreement with experiments for a range of temperatures.

Slipids is compatible with FFs from the AMBER family for amino acids. Tests with AMBER99SB, AMBER99SB-ILDN and AMBER03 together with Slipids have been performed with microsecond simulations and show that they can be mixed. Free energies of transfer of amino acid analogues from water to cyclohexane has also been calculated and are in good agreement with experimental data.

See http://people.su.se/~jjm for more parameters and related data such as structures etc.


Jämbeck JP, Lyubartsev AP, Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids., J Phys Chem B 116 (2012), 3164-79, doi: 10.1021/jp212503e, pubmed:22352995 [pubmed] [hubmed]
Primary Experimental

Jämbeck, J. P. M. and Lyubartsev, A. P., An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes, J. Chem. Theory Comput. (2012), doi: 10.1021/ct300342n, [no pubmed id]
Primary Experimental

Jämbeck, J. P. M. and Lyubartsev, A. P., Another Piece of the Membrane Puzzle: Extending Slipids Further, J. Chem. Theory Comput. (2012), doi: 10.1021/ct300777p, [no pubmed id]
Primary Experimental


Version 2
forcefield.ff.zip 7a30a7aaa40b5dca0070efad5ad847c95d662b26
PDB structure
Bilayer structure
Version 1
POPE.itp ab944bb9b03f504e7ca048f19183e7a7b8bee206
forcefield.ff.zip 472f61e116bf906d6db10914e61fac037c832632
PDB structure
Bilayer structure
POPE.gro 0f159c2ad7ba5e63d120cb72913030d82232503e
POPE.pdb e218b0e3007488ef18150eec3959c534e03e8054