List of all available packages

This is an overview over all 89 packages in the database. Detailed information can be found within each package.

The View button opens the detailed package view, showing all available versions and leading to the user comments for each version. Download latest version immediately downloads a zip file of the latest version of the package that includes a file citations.txt with references and SHA1 checksums for all included files. The Discussion button brings you to the user comments of the latest package version; the total number of comments is shown in brackets.

CHARMM27 Charmm
POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol)

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Lipid POPG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Forcefield CHARMM27
Code Charmm
Authors Hyunbum Jang, Naveen Michaud-Agrawal, Jennifer M Johnston, and Thomas B Woolf
Licence Public Domain Open Knowledge
Curator Oliver Beckstein
Creation date 21 Aug 2009

POPG parameters as used in Jang et al, Proteins 72 (2008), 299. Parameters did not appear in the paper but were obtained from the authors directly. (OB:changed HAL -> HAL1, HAL2 for use with par_all27_lipid.prm)

 [read more]

Martini Gromacs
*PG (*phosphoglycerol )

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Lipid *PG *phosphoglycerol
Forcefield Martini
Code Gromacs
Authors Baoukina S, Monticelli L, Amrein M, and Tieleman DP.
Licence Public Domain Open Knowledge
Curator Benjamin Hall
Creation date 26 Aug 2009
ITP from Luca Monticelli adding parameters for *PG lipids.  [read more]

Bondini Gromacs
*PG (*phosphoglycerol )

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Lipid *PG *phosphoglycerol
Forcefield Bondini
Code Gromacs
Authors Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, and Sansom MS.
Licence Public Domain Open Knowledge
Curator Benjamin Hall
Creation date 26 Aug 2009
ITP for PG lipids used in Bondini (a coarse grained force field based on SJ Marrink's lipid CG force field (later developed into MARTINI), which includes CG particles for amino acids, including an Nm type to give the backbone residues appropriate hydrophilicity) [read more]

Martini Gromacs
*PG (*phosphoglycerol )

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Lipid *PG *phosphoglycerol
Forcefield Martini
Code Gromacs
Authors -
Licence Public Domain Open Knowledge
Curator Benjamin Hall
Creation date 26 Aug 2009
ITP file for *PG lipids based on a port of Scott parameters from Bondini [read more]

GROMOS53a6 Gromacs
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

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Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors A Kukol
Licence fair use
Curator Andreas Kukol
Creation date 31 Aug 2009
Lipid parameters of Kukol, JCTC 5 (2009), 615: United atom (UA) lipids were constructed from the GROMOS 53a6 atom types. Experimental areas per lipid are reproduced to within 3% for DPPC without application of surface tension, and 1.5% for POPC. Parameters were copied directly from the supplementary information available from 10.1021/ct8003468 ([read more]

GROMOS53a6 Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors A Kukol
Licence fair use
Curator Andreas Kukol
Creation date 31 Aug 2009
Lipid parameters of Kukol, JCTC 5 (2009), 615: United atom (UA) lipids were constructed from the GROMOS 53a6 atom types. Experimental areas per lipid are reproduced to within 3% for DPPC without application of surface tension, and 1.5% for POPC. Parameters were copied directly from the supplementary information available from 10.1021/ct8003468 ([read more]

GROMOS53a6 Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors A Kukol
Licence fair use
Curator Andreas Kukol
Creation date 31 Aug 2009
Lipid parameters of Kukol, JCTC 5 (2009), 615: United atom (UA) lipids were constructed from the GROMOS 53a6 atom types. Experimental areas per lipid are reproduced to within 3% for DPPC without application of surface tension, and 1.5% for POPC. Parameters were copied directly from the supplementary information available from 10.1021/ct8003468 ([read more]

GROMOS53a6 Gromacs
POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol)

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Lipid POPG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Forcefield GROMOS53a6
Code Gromacs
Authors A Kukol
Licence fair use
Curator Andreas Kukol
Creation date 31 Aug 2009
D-POPG and L-POPG (the bilayer appears to be pure D-POPG). Lipid parameters of Kukol, JCTC 5 (2009), 615: United atom (UA) lipids were constructed from the GROMOS 53a6 atom types. Experimental areas per lipid are reproduced to within 3% for DPPC without application of surface tension, and 1.5% for POPC. Parameters were copied directly [...] [read more]

GROMOS43a1 Gromacs
1OCT (1-octanol)

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Lipid 1OCT 1-octanol
Forcefield GROMOS43a1
Code Gromacs
Authors Magdalena Elzbieta Siwko
Licence fair use
Curator Oliver Beckstein
Creation date 31 Aug 2009

1-Octanol from Magdalena Elzbieta Siwko's thesis (Appendix A.3) Taken from 06_appendix.pdf (Archived by WebCite® at http://www.webcitation.org/5tY9oUiVa). Comment characters added where necessary (OB 2009-08-12).

Validation (as shown in the thesis):MD density (neat octanol at 298K): 829.1 ± 0.1 g/l. Experiment [1]: 827 g/l

[1] CRC handbook of [...] [read more]

GROMOS43a1 Gromacs
1OCT (1-octanol)

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Lipid 1OCT 1-octanol
Forcefield GROMOS43a1
Code Gromacs
Authors David van der Spoel
Licence Public Domain Open Knowledge
Curator Oliver Beckstein
Creation date 31 Aug 2009
Parameters were copied and pasted from David van der Spoel's message on the gromacs-users mailing list [gmx-users] Do I need to add hydrogens?. From the context it appears that these parameters are to be used with GROMOS96 ffG43a1 but this is not explicitly stated. USE AT YOUR OWN RISK. [read more]

GROMOS53a6 Gromacs
DPhyPC (1,2-diphytanoyl-sn-glycero-3-phosphocholine)

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Lipid DPhyPC 1,2-diphytanoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario
Creation date 04 Sep 2009
Please check the stereochemistry of the glycerol backbone before simulating! Check the R/S configuration. If it's the correct one you want then go ahead and simulate! I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer [...] [read more]

GROMOS53a6 Gromacs
DPhPG (2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol)

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Lipid DPhPG 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario
Creation date 16 Sep 2009
This is an Archaeal lipid found in the Purple Membrane I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer (all done with a bit of editconf!). You then have a more or less regular looking bilayer- add [...] [read more]

GROMOS53a6 Gromacs
DPhPGP-Me (2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-phosphomethyl)

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Lipid DPhPGP-Me 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-phosphomethyl
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario
Creation date 16 Sep 2009
This is an Archaeal lipid found in the Purple Membrane I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer (all done with a bit of editconf!). You then have a more or less regular looking bilayer- add [...] [read more]

GROMOS53a6 Gromacs
DPhPGS (2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-sulphate)

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Lipid DPhPGS 2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol 1'-sulphate
Forcefield GROMOS53a6
Code Gromacs
Authors D'Rozario R
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Robert D'Rozario
Creation date 16 Sep 2009
This is an Archaeal lipid found in the Purple Membrane I created the bilayer by setting up an 8x8 DPhPC leaflet then copy and rotate by 180 deg to get your bottom layer (all done with a bit of editconf!). You then have a more or less regular looking bilayer- add [...] [read more]

CHARMM27 NAMD
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield CHARMM27
Code NAMD
Authors -
Licence Public Domain Open Knowledge
Curator Philip Fowler
Creation date 11 Nov 2009

modified CHARMM27 POPC parameters The IC (internal coordinates) rows in the POPC residue are incorrect. Usually this is not a problem but if one is adding hydrogens and getting psfgen to guess their positions then the errors in the IC rows will cause the hydrogens to be added in [...] [read more]

GROMOS43a1 Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43a1
Code Gromacs
Authors Tieleman DP
Licence fair use
Curator Phill Stansfeld
Creation date 11 Dec 2009

Parameters taken from lipid.itp found at: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies POPC bilayer self-assembled using CG then converted to atomistic by CG2AT. Atomistic bilayer equilibrated though 10 ns of MD.

 [read more]

GROMOS43a1 Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43a1
Code Gromacs
Authors Tieleman DP
Licence fair use
Curator Phill Stansfeld
Creation date 11 Dec 2009
Parameters taken from lipid.itp found at: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies DPPC bilayer self-assembled using CG then converted to atomistic by CG2AT. Atomistic bilayer equilibrated though 10 ns of MD. [read more]

GROMOS43a1 Gromacs
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

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Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43a1
Code Gromacs
Authors Tieleman DP
Licence fair use
Curator Phill Stansfeld
Creation date 11 Dec 2009
Parameters taken from lipid.itp found at: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies DMPC bilayer self-assembled using CG then converted to atomistic by CG2AT. Atomistic bilayer equilibrated though 10 ns of MD. [read more]

GROMOS43a1 Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43a1
Code Gromacs
Authors Tieleman DP
Licence fair use
Curator Phill Stansfeld
Creation date 11 Dec 2009
Parameters taken from lipid.itp found at: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies DOPC bilayer self-assembled using CG then converted to atomistic by CG2AT. Atomistic bilayer equilibrated though 10 ns of MD. [read more]

Bondini Gromacs
POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol)

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Lipid POPG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Forcefield Bondini
Code Gromacs
Authors Wee CL, Gavaghan D, and Sansom MS.
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Chze Ling Wee
Creation date 17 Feb 2010
POPG lipid to be used with SJ Marrink's CG lipid parameters as described in: S.J. Marrink, A.H. de Vries, A.E. Mark. Coarse grained model for semi-quantitative lipid simulations. J. Phys. Chem. B, 108:750-760, 2004. [read more]

Martini Gromacs
DPG (cardiolipin)

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Lipid DPG cardiolipin
Forcefield Martini
Code Gromacs
Authors Martin Dahlberg and Arnold Maliniak
Licence fair use
Curator Joseph Goose
Creation date 06 May 2010

A coarse-grained molecular dynamics model was used to investigate the mechanical properties of cardiolipin bilayers, systematically varying the headgroup charge and the composition in mixtures with zwitterionic 1,2-dioleoyl-glycero-3-phosphatidylcholine (DOPC) or 1,2-dioleoyl-glycero-3-phosphatidylethanolamine (DOPE).

 [read more]

AMBER-GAFF Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Gromacs
Authors Siu SW, Vácha R, Jungwirth P, Böckmann RA.
Licence fair use
Curator Oliver Beckstein
Creation date 19 Jul 2010

Topology files of General AMBER force field for DOPC. Includes simulation snapshot of 72 DOPC, 2727 SOL @100ns at 310K 

  • SPC/E, NPT ensemble: gaff-NPT-100ns.pdb
  • SPC/E, NPγT ensemble (γ=22dyn/cm): gaff-s22-100ns.pdb
  • TIP3P, NPγT ensemble (γ=22dyn/cm): gaff-s22-tip3p-100ns.pdb

Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a [...] [read more]

CHARMM27 Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield CHARMM27
Code Gromacs
Authors Siu SW, Vácha R, Jungwirth P, Böckmann RA
Licence fair use
Curator Oliver Beckstein
Creation date 19 Jul 2010

Topology files of CHARMM27 force field for DOPC. Includes simulation snapshot of 72 DOPC, 2727 TIP3P @100ns at 310K NPγT ensemble (γ=22dyn/cm).

Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force [...] [read more]

GROMOS53a6 Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors Siu SW, Vácha R, Jungwirth P, Böckmann RA
Licence fair use
Curator Oliver Beckstein
Creation date 19 Jul 2010

Topology files of Berger force field combined in GROMOS96 (ffG53a6) for DOPC. Includes simulation snapshot of 128 DOPC, 4789 SPC @100ns at 310K NPT ensemble.

Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom [...] [read more]

GROMOS53a6 Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein
Creation date 03 Aug 2010

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by [...] [read more]

GROMOS53a6 Gromacs
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

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Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein
Creation date 03 Aug 2010

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by [...] [read more]

GROMOS53a6 Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein
Creation date 03 Aug 2010

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by [...] [read more]

GROMOS53a6 Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein
Creation date 03 Aug 2010

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, using a recent revision of the GROMOS96 force field (53a6) are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy.

The [read more]

GROMOS53a6 Gromacs
DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine)

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Lipid DLPC 1,2-dilauroyl-sn-glycero-3-phosphocholine
Forcefield GROMOS53a6
Code Gromacs
Authors David Poger, Alan E. Mark
Licence fair use
Curator Oliver Beckstein
Creation date 05 Aug 2010

Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by [...] [read more]

Martini Gromacs
chol (cholesterol)

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Lipid chol cholesterol
Forcefield Martini
Code Gromacs
Authors Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Oliver Beckstein
Creation date 03 Oct 2010

Coarse grained cholesterol, linked from SJ Marrink's parameter website. (ITP file contains CHOLESTEROL, CHOLESTERYL OLEATE, CHOLATE). See the website for mixed bilayers and example input files.

 

 [read more]

Martini Gromacs
DUPC (1,2-(cis-cis-9,12-octadecadienoyl)-sn-glycero-3-phosphatidylcholine)

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Lipid DUPC 1,2-(cis-cis-9,12-octadecadienoyl)-sn-glycero-3-phosphatidylcholine
Forcefield Martini
Code Gromacs
Authors Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Jan Domanski
Creation date 22 Jan 2011

Doubly unsaturated DUPC. The lipid can be used in ternary mixture with DPPC and CHOL, which undergoes phase-separation. An example of a mixed and phase-separated bilayer is attached.

Note(s):

files have been taken from http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters
the DPPC and cholesterol topologies can be found there together with the other martini parameters

 

 [read more]

Martini Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield Martini
Code Gromacs
Authors Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Jan Domanski
Creation date 26 Jan 2011

diC(16:0)-PC - DPPC - topology for MARTINI. The package includes a 128-DPPC bilayer patch.

 [read more]

GROMOS87 Gromacs
chol (cholesterol)

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Lipid chol cholesterol
Forcefield GROMOS87
Code Gromacs
Authors Höltje M, Förster T, Brandt B, Engels T, von Rybinski W, Höltje HD
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Jan Domanski
Creation date 02 Mar 2011

Cholesterol atomistic parameters developed by Monika Hoeltje and Birte Brandt (September 1998), using a force-field parameters developed by Peter Tieleman.

The lipid.itp comes from P. Tieleman's lab webpage.
The ffgmx*.* are the gromos parameters (come with Gromacs package). Both of these files are the versions available in [...] [read more]

GROMOS87 Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS87
Code Gromacs
Authors Niemelä PS, Ollila S, Hyvönen MT, Karttunen M, Vattulainen I
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Jan Domanski
Creation date 02 Mar 2011

POPC atomistic parameters developed by Peter Tieleman.

The lipid.itp comes from P. Tieleman's lab webpage.
The ffgmx*.* are the gromos parameters (come with Gromacs package). Both of these files are the versions available in 2007.

 [read more]

GROMOS87 Gromacs
SM (D-erythro-n-palmitoyl-sphingomyelin)

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Lipid SM D-erythro-n-palmitoyl-sphingomyelin
Forcefield GROMOS87
Code Gromacs
Authors Niemelä PS, Ollila S, Hyvönen MT, Karttunen M, Vattulainen I
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Jan Domanski
Creation date 02 Mar 2011

Sphingomyelin atomistic parameters developed by Perttu Niemelä and Ilpo Vattulainen.

For validation of the parameters, see:
Niemelä P, Hyvönen MT, Vattulainen I (2004) Structure and dynamics of
sphingomyelin bilayer: Insight gained through systematic comparison to
phosphatidylcholine. Biophys J 87: 2976–2989.

The lipid.itp comes from [...] [read more]

CHARMM36 Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield CHARMM36
Code Gromacs
Authors Klauda, Jeffery B and Venable, Richard M and Freites, J Alfredo and O'Connor, Joseph W and Tobias, Douglas J and Mondragon-Ramirez, Carlos and Vorobyov, Igor and MacKerell, Jr, Alexander D and Pastor, Richard W
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Rongliang Wu
Creation date 06 Mar 2012

156 POPE lipids equilibrated for 40 ns

surface per lipid 0.572 nm^2

 

 [read more]

AMBER-GAFF Gromacs
1OCT (1-octanol)

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Lipid 1OCT 1-octanol
Forcefield AMBER-GAFF
Code Gromacs
Authors Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D
Licence fair use
Curator Oliver Beckstein
Creation date 23 Mar 2012

1-octanol from virtualchemistry.org, validated liquid properties:

  • density
  • enthalpy of vaporization
  • surface tension
  • static dielectric constant
  • volumetric expansion coefficient
  • isothermal compressibility
  • heat capacity at constant volume
  • classical heat capacity at constant pressure
 [read more]

OPLS Gromacs
1OCT (1-octanol)

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Lipid 1OCT 1-octanol
Forcefield OPLS
Code Gromacs
Authors Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D
Licence fair use
Curator Oliver Beckstein
Creation date 23 Mar 2012

1-octanol from virtualchemistry.org, validated liquid properties:

  • density
  • enthalpy of vaporization
  • surface tension
  • static dielectric constant
  • volumetric expansion coefficient
  • isothermal compressibility
  • heat capacity at constant volume
  • classical heat capacity at constant pressure
 [read more]

OPLS Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield OPLS
Code Gromacs
Authors Jakob P. Ulmschneider and Martin B. Ulmschneider
Licence fair use
Curator Martin Ulmschneider
Creation date 20 Apr 2012

OPLS-UA lipids consistent with the OPLS-AA force field.

Please cite: J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813

 [read more]

OPLS Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion (1)
Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield OPLS
Code Gromacs
Authors Jakob P. Ulmschneider and Martin B. Ulmschneider
Licence fair use
Curator Martin Ulmschneider
Creation date 20 Apr 2012

OPLS-UA lipids consistent with the OPLS-AA force field.

Please cite: J.P. Ulmschneider & M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field, JCTC 2009, 5(7), 1803–1813

 [read more]

Slipids/AMBER Gromacs
DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DLPC 1,2-dilauroyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 02 May 2012

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 [...] [read more]

Slipids/AMBER Gromacs
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 02 May 2012

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 [...] [read more]

Slipids/AMBER Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 02 May 2012

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 [...] [read more]

GROMOS-CKP Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

POPE GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.

If you use these parameters please read and cite:

Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex [...] [read more]

GROMOS-CKP Gromacs
DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion (1)
Lipid DPPE 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

DPPE GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.


If you use these parameters please read and cite:


Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics [...] [read more]

GROMOS-CKP Gromacs
POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol)

Show package Download latest version Discussion
Lipid POPG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

POPG GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.


If you use these parameters please read and cite:


Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics [...] [read more]

GROMOS-CKP Gromacs
DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol)

Show package Download latest version Discussion
Lipid DMPG 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

DMPG GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.


If you use these parameters please read and cite:


Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics [...] [read more]

GROMOS-CKP Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Piñeiro Á, Khalid S.
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

POPC GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.

If you use these parameters please read and cite:

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. Thomas J. Piggot, Ángel [...] [read more]

GROMOS-CKP Gromacs
POPO (1',3'-bis[1-palmitoyl,2-oleoyl-sn-glycero-3-phospho]-sn-glycerol)

Show package Download latest version Discussion
Lipid POPO 1',3'-bis[1-palmitoyl,2-oleoyl-sn-glycero-3-phospho]-sn-glycerol
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 22 May 2012

POPO Cardiolipin GROMOS-CKP lipid parameters. These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.


If you use these parameters please read and cite:


Electroporation of the E. coli and S. aureus Membranes: Molecular [...] [read more]

GROMOS-CKP Gromacs
Lipid A (Lipid A (E. coli))

Show package Download latest version Discussion
Lipid Lipid A Lipid A (E. coli)
Forcefield GROMOS-CKP
Code Gromacs
Authors Piggot TJ, Holdbrook DA, Khalid S
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 30 May 2012

GROMOS E. coli Lipid A parameters. These parameters can be used with the GROMOS 53A6 protein force field without any modification to the parameters. They can also be combined with the GROMOS-CKP phospholipid parameters.


If you use these parameters please read and cite:


Electroporation of [...] [read more]

GROMOS43A1-S3 Gromacs
DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DLPC 1,2-dilauroyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 31 May 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
chol (cholesterol)

Show package Download latest version Discussion
Lipid chol cholesterol
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane compositions in semi-isotropic NTP [...] [read more]

GROMOS43A1-S3 Gromacs
SMGL (18:0 SM (d18:1/18:0) N-stearoyl-D-erythro-sphingosylphosphorylcholine)

Show package Download latest version Discussion
Lipid SMGL 18:0 SM (d18:1/18:0) N-stearoyl-D-erythro-sphingosylphosphorylcholine
Forcefield GROMOS43A1-S3
Code Gromacs
Authors Chiu SW, Pandit SA, Scott HL, Jakobsson E
Licence fair use
Curator Oliver Beckstein
Creation date 01 Jun 2012

18:0 SM (d18:1/18:0) sphingomyelin

A new GROMOS43a1-based force field (43A1-S3) for simulation of membranes with the  Gromacs simulation package. The validity of the force fields is demonstrated by correct replication of X-ray form factors and NMR order parameters over a wide range of membrane [...] [read more]

Slipids/AMBER Gromacs
DLPE (1,2-dilauroyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid DLPE 1,2-dilauroyl-sn-glycero-3-phosphoethanolamine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

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 [...] [read more]

Slipids/AMBER Gromacs
DOPE (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid DOPE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck, J. P. M. and Lyubartsev, A. P.
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

An all-atomistic force field (FF) for saturated PC [...] [read more]

Slipids/AMBER Gromacs
DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid DPPE 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

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 [...] [read more]

Slipids/AMBER Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

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 [...] [read more]

Slipids/AMBER Gromacs
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

Show package Download latest version Discussion
Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

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 [...] [read more]

Slipids/AMBER Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

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 [...] [read more]

Slipids/AMBER Gromacs
SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid SOPC 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 14 Jul 2012

 

[read more]

GROMOS-CKP Gromacs
PI(4,5)P2 (1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate))

Show package Download latest version Discussion
Lipid PI(4,5)P2 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-myo-inositol-4',5'-bisphosphate)
Forcefield GROMOS-CKP
Code Gromacs
Authors Holdbrook DA, Leung YM, Piggot TJ, Marius P, Williamson PT, Khalid S.
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Tom Piggot
Creation date 14 Sep 2012

PI(4,5)P2 GROMOS-CKP lipid parameters (with dipalmitoyl tails). These lipid parameters can be used with the GROMOS 53A6 and GROMOS 54A7 protein force fields without any modifications to the parameters.

If you use these parameters please read and cite:

For the headgroup:

Stability and Membrane Orientation of the Fukutin Transmembrane [...] [read more]

Slipids/AMBER Gromacs
chol (cholesterol)

Show package Download latest version Discussion
Lipid chol cholesterol
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DLPG (1,2-dilauroyl-sn-glycero-3-phospho-(1'-rac-glycerol))

Show package Download latest version Discussion
Lipid DLPG 1,2-dilauroyl-sn-glycero-3-phospho-(1'-rac-glycerol)
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol)

Show package Download latest version Discussion
Lipid DMPG 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DOPG (1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1'-rac-glycerol) )

Show package Download latest version Discussion
Lipid DOPG 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1'-rac-glycerol)
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DOPS (1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine)

Show package Download latest version Discussion
Lipid DOPS 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DPPG (1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol)

Show package Download latest version Discussion
Lipid DPPG 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
DSPG (1,2-distearoyl-sn-glycero-3-phospho-(1'-rac-glycerol) )

Show package Download latest version Discussion
Lipid DSPG 1,2-distearoyl-sn-glycero-3-phospho-(1'-rac-glycerol)
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol)

Show package Download latest version Discussion
Lipid POPG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
SM (D-erythro-n-palmitoyl-sphingomyelin)

Show package Download latest version Discussion
Lipid SM D-erythro-n-palmitoyl-sphingomyelin
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck JP, Lyubartsev AP
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

Slipids/AMBER Gromacs
SMGL (18:0 SM (d18:1/18:0) N-stearoyl-D-erythro-sphingosylphosphorylcholine)

Show package Download latest version Discussion (1)
Lipid SMGL 18:0 SM (d18:1/18:0) N-stearoyl-D-erythro-sphingosylphosphorylcholine
Forcefield Slipids/AMBER
Code Gromacs
Authors Jämbeck, J. P. M. and Lyubartsev, A. P.
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Joakim Jämbeck
Creation date 10 Nov 2012

See http://people.su.se/~jjm/Stockholm_Lipids/Home.html for for more details and structure files to download

 [read more]

GROMOS53a6 Gromacs
Lipid_A (Lipid A (P. aeruginosa))

Show package Download latest version Discussion
Lipid Lipid_A Lipid A (P. aeruginosa)
Forcefield GROMOS53a6
Code Gromacs
Authors Frederico J. S. Pontes, Victor H. Rusu, Thereza A. Soares, and Roberto D. Lins
Licence CreativeCommons Attribution-ShareAlike licence 3.0 Open Knowledge
Curator Frederico José de Santana Pontes
Creation date 20 Dec 2012

This file contains the topologies and coordinates of Lipid A (hexa- and pentaacylated species) for Pseudomonas aeruginosa bacteria. The force field is a extension of the GROMOS force field combinated with the 45a4 carbohydrate parameter set and are in the GROMACS format of topologies. [...] [read more]

OPLS Gromacs
DDM (dodecyl maltoside)

Show package Download latest version Discussion
Lipid DDM dodecyl maltoside
Forcefield OPLS
Code Gromacs
Authors -
Licence Public Domain Open Knowledge
Curator S Rouse
Creation date 14 May 2013

No abstract present for this package

 [read more]

Martini Gromacs
DDM (dodecyl maltoside)

Show package Download latest version Discussion
Lipid DDM dodecyl maltoside
Forcefield Martini
Code Gromacs
Authors -
Licence Public Domain Open Knowledge
Curator S Rouse
Creation date 14 May 2013

No abstract present for this package

 [read more]

AMBER-GAFF Amber
DLPC (1,2-dilauroyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DLPC 1,2-dilauroyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of DLPC using AMBER. Also included are PDB files of 72, 288 and 2x288 DLPC bilayers.

 

To unzip: tar -xvzf DLPC.tgz

 [read more]

AMBER-GAFF Amber
DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DMPC 1,2-dimyristoyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of DMPC using AMBER. Also included are PDB files of 72, 288 and 2x288 DMPC bilayers.

 

To unzip: tar -xvzf DMPC.tgz

 [read more]

AMBER-GAFF Amber
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

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Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of DPPC using AMBER. Also included are PDB files of 72, 288 and 2x288 DPPC bilayers.

 

To unzip: tar -xvzf DPPC.tgz

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AMBER-GAFF Amber
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of DOPC using AMBER. Also included are PDB files of 72, 288 and 2x288 DOPC bilayers.

 

To unzip: tar -xvzf DOPC.tgz

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AMBER-GAFF Amber
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of POPC using AMBER. Also included are PDB files of 72, 288 and 2x288 POPC bilayers.

 

To unzip: tar -xvzf POPC.tgz

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AMBER-GAFF Amber
POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine)

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Lipid POPE 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
Forcefield AMBER-GAFF
Code Amber
Authors -
Licence Public Domain Open Knowledge
Curator Callum Dickson
Creation date 09 Oct 2013

GAFFlipid parameter files for simulation of POPE using AMBER. Also included are PDB files of 72, 288 and 2x288 POPE bilayers.

 

To unzip: tar -xvzf POPE.tgz

 [read more]

Martini Gromacs
POPC (1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine)

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Lipid POPC 1-palmitoyl,2-oleoyl-sn-glycero-3-phosphocholine
Forcefield Martini
Code Gromacs
Authors Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA
Licence fair use
Curator Jan Domanski
Creation date 29 Oct 2014

Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop [...] [read more]

Martini Gromacs
chol (cholesterol)

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Lipid chol cholesterol
Forcefield Martini
Code Gromacs
Authors Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA
Licence fair use
Curator Jan Domanski
Creation date 29 Oct 2014

Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop [...] [read more]

Martini Gromacs
DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DPPC 1,2-dipalmitoyl-sn-glycero-3-phosphocholine
Forcefield Martini
Code Gromacs
Authors Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA
Licence fair use
Curator Jan Domanski
Creation date 29 Oct 2014

Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop [...] [read more]

Martini Gromacs
DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

Show package Download latest version Discussion
Lipid DOPC 1,2-dioleoyl-sn-glycero-3-phosphocholine
Forcefield Martini
Code Gromacs
Authors Daily MD, Olsen BN, Schlesinger PH, Ory DS, Baker NA
Licence fair use
Curator Jan Domanski
Creation date 29 Oct 2014

Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop [...] [read more]