List of all available packages

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)

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]

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]

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.

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).

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]

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]

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]

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]

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]

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]

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]

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]

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.

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

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

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]

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.

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]

156 POPE lipids equilibrated for 40 ns

surface per lipid 0.572 nm^2

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

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

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

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

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]

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]

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]

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]

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]

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 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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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

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

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

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

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

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

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

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

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

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

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]

No abstract present for this package

No abstract present for this package

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

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

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

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

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

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

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]

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]

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]

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]