Downloads, Stockholm lipids
Downloads, Stockholm lipids
Here we share Slipids force field parameters in
GROMACS
format, ready to use as well as equilibrated lipid bilayers.
Parameters are available for saturated and unsaturated PC, PS, PE, PG, SM lipids and cholesterol. They are supposed to work with AMBER99SB/AMBER99SB-ILDN/AMBER03/GAFF FF for proteins and small molecules.
Cannot find the lipid bilayer composition you are looking for? Go over to MemGen or CHARMM-GUI and use their interface to built your system.
To study proteins in membranes just add our parameters to the AMBER protein force field you would like to use. We have verified the compatibility by calculating both free energies of transfer of amino acid analogues and microsecond long simulations of the WALP23 helix embedded in a lipid bilayer.
Please feel free to use these parameters and/or coordinates for you own projects, but make sure you cite the following references:
Saturated PC lipids:
Joakim P. M. Jämbeck, Alexander P. Lyubartsev, J. Phys. Chem. B, 2012, 116 (10), 3164-3179
DOI: 10.1021/jp212503e
POPC, DOPC, SOPC, DOPE, POPE and similar:
An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes, Joakim P. M. Jämbeck, Alexander P. Lyubartsev, J. Chem. Theory Comput., 8 (8), 2938-2948 DOI: 10.1021/ct300342n
PS, PG, SM lipids and Cholesterol:
Another Piece of the Membrane Puzzle: Extending Slipids Further,
Joakim P. M. Jämbeck, Alexander P. Lyubartsev, J. Chem. Theory Comput., 9 (1), 774-784 (2013)
DOI: 10.1021/ct300777p
Polyunsaturated lipids:
Extension of the Slipids Force Field for Polyunsaturated Lipids,
Inna Ermilova, Alexander P. Lyubartsev, J. Phys. Chem. B, 120 (50), pp 12826–12842 (2016)
DOI: 10.1021/acs.jpcb.6b05422
Slipids update 2020:
Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids,
Fredrik Grote, Alexander P. Lyubartsev, J. Phys. Chem. B, 124 (50), pp 8784-8793 (2020)
DOI: 10.1021/acs.jpcb.0c06386
The authors thank Yeol Kyo Choi for careful checking of the lipids topology files and suggested corrections.
Contact us if you have any suggestions and/or questions.
Files to download
Full Slipids-2020 archive
All Slipids parameters with the itp- and pdb- files for selected lipids and examples of simulation boxes
Force field parameters only
itp and pdb files
• cholesterol.itp ; cholesterol.pdb (cholesterol)
• TIP3p.itp (TIP3P water)
(Water model used in the verification, feel free to try other models but make sure that you validate your simulations carefully)
Sample topology file
Pre-equilibrated boxes
Snapshots after 400/500 ns long simulations, all boxes are with 128 lipids (cholesterol considered to be a lipid)
• DLPC
303 K (DLPC_303K.pdb), 323 K (DLPC_323K.gro, DLPC_323K.pdb)
333 K (DLPC_333K.gro, DLPC_333K.pdb)
• DLPE
308 K (DLPE_H2O.gro, DLPE_H2O.pdb)
• DLPG
293 K (DLPG_293K.gro), 303 K (DLPG_303K.gro), 323 K (DLPG_323K.gro),
333 K (DLPG_333K.gro)
• DMPC
303 K (DMPC_303K.gro, DMPC_303K.pdb), 323 K (DMPC_323K.gro, DMPC_323K.pdb)
333 K (DMPC_333K.gro, DMPC_333K.pdb)
303 K, 10% cholesterol (DMPC_0.1chl.gro)
303 K, 20% cholesterol (DMPC_0.2chl.gro)
303 K, 30% cholesterol (DMPC_0.3chl.gro)
303 K, 40% cholesterol (DMPC_0.4chl.gro)
303 K, 50% cholesterol (DMPC_0.5chl.gro)
• DMPG
303 K (DMPG_303K.gro), 323 K (DMPG_323K.gro)
• DPPC
293 K (DPPC_293K.gro, DPPC_293K.pdb), 323 K (DPPC_323K.gro, DPPC_323K.pdb)
333 K (DPPC_333K.gro, DPPC_333K.pdb), 353 K (DPPC_353K.gro, DPPC_353K.pdb)
• DPPE
343 K (DPPE_H2O.gro, DPPE_H2O.pdb)
• DPPG
323 K (DPPG_323K.gro), 333 K (DPPG_333K.gro)
• DSPG
333 K (DSPG_333K.gro)
• POPC
293 K (POPC_293K.gro, POPC_293K.pdb), 303 K (POPC_303K.gro, POPC_303K.pdb)
323 K (POPC_323K.gro, POPC_323K.pdb), 333 K (POPC_333K.gro, POPC_333K.pdb)
• POPE
303 K (POPE_H2O.gro, POPE_H2O.pdb)
• POPG
293 K (POPG_293K.gro), 303 K (POPG_303K.gro) 323 K (POPG_323K.gro)
333 K (POPG_333K.gro)
• DOPC
293 K (DOPC_293K.gro, DOPC_293K.pdb), 303 K (DOPC_303K.gro, DOPC_303K.pdb)
323 K (DOPC_323K.gro, DOPC_323K.pdb), 333 K (DOPC_333K.gro, DOPC_333K.pdb)
303 K, 10% cholesterol (DOPC_0.1chl.gro)
303 K, 20% cholesterol (DOPC_0.2chl.gro)
303 K, 30% cholesterol (DOPC_0.3chl.gro)
303 K, 40% cholesterol (DOPC_0.4chl.gro)
303 K, 50% cholesterol (DOPC_0.5chl.gro)
• DOPE
271 K (DOPE_271K.gro)
• DOPG
293 K (DOPG_293K.gro), 303 K (DOPG_303K.gro), 323 K (DOPG_323K.gro)
353 K (DOPG_333K.gro)
• DOPS
303 K (DOPS_303K.gro)
• SOPC
293 K (SOPC_293K.gro, SOPC_293K.pdb), 303 K (SOPC_303K.gro, SOPC_303K.pdb)
323 K (SOPC_323K.gro, SOPC_323K.pdb), 333 K (SOPC_333K.gro, SOPC_333K.pdb)
303 K, 10% cholesterol (SOPC_0.1chl.gro)
303 K, 20% cholesterol (SOPC_0.2chl.gro)
303 K, 30% cholesterol (SOPC_0.3chl.gro)
303 K, 40% cholesterol (SOPC_0.4chl.gro)
303 K, 50% cholesterol (SOPC_0.5chl.gro)
• 16:0 sphingomyelin
323 K (16SM.gro)
323 K, 20 % cholesterol (16SM_0.2chl.gro)
•18:0 sphingomyelin
323 K (18SM.gro)
• Smaller membrane patches (good for PMF calculations etc.)
DMPC_64_303K.gro (run this a bit longer to make sure that the system is in equilibrium)
example of mdp file
• md.mdp