DOI: 10.5281/zenodo.1149622
title: Slipids Force Field  V2.0 (2016)

description: Slipids force field:  files for Gromacs<br>
-----------------------------------------------------------

Authors:  Joakim Jämbeck, Inna Ermilova, Alexander Lyubartsev<br>
      Department of Materials and Environmental Chemistry,<br>
      Stockholm University,  Stockholm   10691  Sweden<br>
      e-mail:  alexander.lyubartsev@mmk.su.se

Content:

SLipids_FF:  directory containing the force field. Included into the Gromacs<br>
         topology file by:  <br>
         #include "SLipids_FF/forcefield.itp"

itp_files:   itp files for various lipids

 

The force field can be used together with the AMBER99SB/AMBER03/GAFF<br>
for proteins

<br>
!!!! MAKE SURE YOU CITE THE FOLLOWING REFERENCES WHEN USING THIS FORCE FIELD !

<br>
Saturated PC lipids:

Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "Derivation and Systematic<br>
Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids",<br>
J. Phys. Chem. B, 2012, 116, 3164-3179 (2012)  DOI: 10.1021/jp212503e

POPC, DOPC, SOPC, DOPE, POPE and similar:<br>
 <br>
Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "An Extension and Further<br>
Validation of an All-Atomistic Force Field for Biological Membranes"<br>
J. Chem. Theory Comput., 8, 2938-2948, (2012) DOI: 10.1021/ct300342n

PS, PG, SM lipids and Cholesterol:

Joakim P. M. Jämbeck and Alexander P. Lyubertsev, "Another Piece of the<br>
Membrane Puzzle: Extending Slipids Further"<br>
J. Chem. Theory Comput.,  9 (1), 774-784 (2013) DOI: 10.1021/ct300777p

Polyinsaturated lipids:

Inna Ermilova and Alexander Lyubartsev:, "Extension of the Slipids Force<br>
Field for Polyunsaturated Lipids",<br>
J. Phys. Chem. B, 120 (50), 12826–12842 (2016)

<br>
Cite also this paper on Charmm36 force field since bond and angle parameters,<br>
as well as a part of Lennard-Jones parameters and torsion angles in the lipid<br>
headgroups in SLipids are taken from the Charmm36 force field:

Jeffery B. Klauda, Richard M. Venable, Alfredo Freites, Joseph W. O’Connor,<br>
Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D.<br>
MacKerell, Jr. and Richard W. Pastor, "Update of the CHARMM all-atom additive<br>
force field for lipids: Validation on six lipid types", J.Phys.Chem B, 114,<br>
7830–78 (2010)
description: Funding: Swedish Research Council (Vetenskapsrådet)
description: {"references": ["Joakim P. M. J\u00e4mbeck and Alexander P. Lyubertsev, \"Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids\", J. Phys. Chem. B, 2012, 116, 3164-3179 (2012)  DOI: 10.1021/jp212503e", "Joakim P. M. J\u00e4mbeck and Alexander P. Lyubertsev, \"An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes\" J. Chem. Theory Comput., 8, 2938-2948, (2012) DOI: 10.1021/ct300342n", "Joakim P. M. J\u00e4mbeck and Alexander P. Lyubertsev, \"Another Piece of the Membrane Puzzle: Extending Slipids Further\" J. Chem. Theory Comput.,  9 (1), 774-784 (2013) DOI: 10.1021/ct300777p", "Inna Ermilova and Alexander Lyubartsev:, \"Extension of the Slipids Force Field for Polyunsaturated Lipids\", J. Phys. Chem. B, 120 (50), 12826\u201312842 (2016)"]}