Site Types for Martini

The table below lists site types to use when drawing molecules in the Coarse-Grained Sketcher for Martini models. Unless otherwise noted Ref. [1] is a good basic source of information.

Chemical name

Site type names, with topology diagram for molecules with multiple sites

Notes

water

W

Single water site representing 4 water molecules.

anitfreeze water

WF

Single water site representing 4 water molecules. Use for 10% of the water present in the system.

sodium ion

Na_ion

 

chlorine ion

Cl_ion

 

calcium ion

Ca_ion

 

cholorform

CLF

 

butane

BUT

Single site representing ~4 carbon atoms with accompanying hydrogens. Can be used as a building block in larger molecules.

ethanol

EOL

 

propanol

POL

 

ether

ETH

 

butanol

BOL

 

acetic acid

ACH

Uncharged acetic acid

benzene

benzene4.png

3 equivalent ring sites are used [2].

chlorobenzene

chlorobenzne.png

2 equivalent ring sites with 1 combined Cl/ring site [3].

cyclohexane

cyclohexane.png

 

octane

octane.png

 

octanol

octanol.png

 

cholesterol

cholesterol.png

 

dodecane

dodecance.png

 

hexadecane

hexadecane.png

 

octadecane

octadecane.png

 

cis-octadecene

cis-octadecene.png

Cis double bond near the middle of the chain.

trans-octadecene

trans-octadecene.png

Trans double bond in the first half of the chain.

dipalmitoyl-phosphatidyl-choline (DPPC)

DPPC.png

In addition to Ref. [1] see also Ref. [4]

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

POPC.png

In addition to Ref. [1] see also Ref. [4]

fructose

fructose.png

See Ref. [5]

glucose

glucose.png

See Ref. [5]

maltose

maltose.png

See Ref. [5]

sucrose

sucrose.png

See Ref. [5]

Polymers

poly(amidoamine)

PAMAM

PAMAM.png

Dendrimer arms can end with either a neutral CH2-C(=O)-N(-H)-CH3 or positively charged CH2-NH3+. See Ref. [6]

poly(oxyethylene) polymers (PEO/PEG)

PEO_PEG.png

Chains can be terminated with either an OH (PEO_SPh, right end) or without (PEO_SP, left end O) [7].

poly(oxyethylene) alkyl ether surfactant

C12_E2.png

Example for C12E2. See Ref. [7].

polystyrene

polystyrene.png

Phenyl rings are represented by 3 STYR_STY sites. Adjacent phenyl rings are linked by STYR_SCY sites [8].

[1] The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations, S. J. Marrink et al., J. Phys. Chem. B 2007, 111, 7812-7824.

[2] Improved Parameters for the Martini Coarse-Grained Protein Force Field, D. H. de Jong et al., J. Chem. Theory Comput. 2012, 9, 687.

[3] Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations, R. Alessandri et al., J. Am. Chem. Soc. 2017, 139, 3697−3705.

[4] Coarse Grained Model for Semiquantitative Lipid Simulations, Siewert J. Marrink et al., J. Phys. Chem. B 2004, 108, 750.

[5] Martini Coarse-Grained Force Field: Extension to Carbohydrates, C. A. López et al., J. Chem. Theory Comput. 2009, 5, 3195.

[6] Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth- and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer, H. Lee et al., J Phys Chem B. 2008, 112, 7778.

[7] A Coarse-Grained MARTINI Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants, G. Rossi et al., J. Phys. Chem. B 2012, 116, 14353.

[8] Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case, Giulia Rossi et al., Soft Matter 2011, 7, 698.

Related Topics