Downloads, Stockholm lipids

Information

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:

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine 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

  1. Slipids_2020.tar.gz


Force field parameters only

  1. Slipids_2020.ff.tar.gz


itp and pdb files

  1. DLPC.itp ; DLPC.pdb (12:0-12:0 PC)

  2. DLPE.itp ; DLPE.pdb (12:0-12:0 PE)

  3. DLPG.itp ; DLPG.pdb (12:0-12:0 PG)

  4. DMPC.itp ; DMPC.pdb (14:0-14:0 PC)

  5. DMPG.itp ; DMPG.pdb (14:0-14:0 PG)

  6. DPPC.itp ; DPPC.pdb (16:0-16:0 PC)

  7. DPPE.itp ; DPPE.pdb (16:0-16:0 PE)

  8. DPPG.itp ; DPPG.pdb (16:0-16:0 PG)

  9. DSPC.itp ; DSPC.pdb (18:0-18:0 PC)

  10. DSPG.itp ; DSPG.pdb (18:0-18:0 PG)

  11. POPC.itp ; POPC.pdb (16:0-18:1(n-9) PC)

  12. POPE.itp ; POPE.pdb (16:0-18:1(n-9) PE)

  13. POPG.itp ; POPG.pdb (16:0-18:1(n-9) PG)

  14. POPS.itp ; POPS.pdb (16:0-18:1(n-9) PS)

  15. SOPC.itp ; SOPC.pdb (18:0-18:1(n-9) PC)

  16. DOPC.itp ; DOPC.pdb (18:1(n-9)-18:1(n-9) PC)

  17. DOPE.itp ; DOPE.pdb (18:1(n-9)-18:1(n-9) PE)

  18. DOPG.itp ; DOPG.pdb (18:1(n-9)-18:1(n-9) PG)

  19. DOPS.itp ; DOPS.pdb (18:1(n-9)-18:1(n-9) PS)

  20. PiLPC.itp ; PiLPC.pdb (16:0-18:2(n-9)PC)

  21. PDPC.itp ; PDPC.pdb (16:0-22:6(n-3)PC)

  22. ENET.itp ; ENET.pdb (18:0-18:3(n-3)PC)

  23. SAPC.itp ; SAPC.pdb (18:0-20:4(n-6)PC)

  24. ENTW.itp ; ENTW.pdb (18:0-20:5(n-3)PC)

  25. ENTF.itp ; ENTF.pdb (18:0-22:5(n-6)PC)

  26. SDPC.itp ; SDPC.pdb (18:0-22:6(n-3)PC; DHA)

  27. DAPC.itp ; DAPC.pdb (20:4(n-6)-20:4(n-6)PC)

  28. DDPC.itp ; DDPC.pdb (22:6(n-3)-22:6(n-3)PC)

  29. SM16.itp ; SM16.pdb (16:0 SM)

  30. SM18.itp ; SM18.pdb (18:0 SM)

  31. cholesterol.itp ; cholesterol.pdb (cholesterol)

  32. 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

  1. sample.top


Pre-equilibrated boxes

Snapshots after 400/500 ns long simulations, all boxes are with 128 lipids (cholesterol considered to be a lipid)

  1. DLPC

303 K (DLPC_303K.pdb), 323 K (DLPC_323K.gro, DLPC_323K.pdb)

333 K (DLPC_333K.gro, DLPC_333K.pdb)


  1. DLPE

308 K (DLPE_H2O.gro, DLPE_H2O.pdb)


  1. DLPG

293 K (DLPG_293K.gro), 303 K (DLPG_303K.gro), 323 K (DLPG_323K.gro),

333 K (DLPG_333K.gro)


  1. 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)


  1. DMPG

303 K (DMPG_303K.gro), 323 K (DMPG_323K.gro)


  1. 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)


  1. DPPE

343 K (DPPE_H2O.gro, DPPE_H2O.pdb)


  1. DPPG

323 K (DPPG_323K.gro), 333 K (DPPG_333K.gro)


  1. DSPG

333 K (DSPG_333K.gro)


  1. 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)


  1. POPE

303 K (POPE_H2O.gro, POPE_H2O.pdb)


  1. POPG

293 K (POPG_293K.gro), 303 K (POPG_303K.gro) 323 K (POPG_323K.gro)

333 K (POPG_333K.gro)


  1. 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)


  1. DOPE

271 K (DOPE_271K.gro)


  1. DOPG

293 K (DOPG_293K.gro), 303 K (DOPG_303K.gro), 323 K (DOPG_323K.gro)

353 K (DOPG_333K.gro)


  1. DOPS

303 K (DOPS_303K.gro)


  1. 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)


  1. 16:0 sphingomyelin

323 K (16SM.gro)

323 K, 20 % cholesterol (16SM_0.2chl.gro)


  1. 18:0 sphingomyelin

323 K (18SM.gro)


  1. 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)

DOPC_64_303K.gro

DPPC_64_323K.gro


example of mdp file

  1. md.mdp