Slipids/AMBER Gromacs by XYZ

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Lipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)
Pubchem CID:26197
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
DMPC.itp 29e7a139c723bb3bf32214181763b48f7bacdecd
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/DMPC.itp WebCiteID:
forcefield.ff.zip d3726c8636c7a86414f40c8f020799cd7c54df17
WebCite:http://web.me.com/jambeck/lipids/Downloads_files/forcefield.ff.zip WebCiteID:
PDB structure
Bilayer structure
DMPC_303K.gro e88007aef9d19c76eea981d27a26e9c03f8711af
WebCite:http://web.me.com/jambeck/lipids/Downloads.html WebCiteID:
DMPC_323K.gro f05e5de7f4a8336dadc9876cc39490c6cd5149c6
DMPC_333K.gro d00d06e8af4e5d51d21ab09e03dc8d1994d8c442