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Forcefield Parameters
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Example of a general input parameter file.
martini_v2.x_example.mdp |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Forcefield Parameters
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Example of a general topology file. Depending on the system, one or several of the molecular topology files should be included (martini_v2.x_*.itp).
martini_v2.x_example.top |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Forcefield Parameters
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Including all common PC and PEs, with hexanoyl, lauroyl, palmitoyl, oleoyl, stearoyl and arachidonoyl tails. Trial topologies for a sphingolipid and for PG and PS lipids are also included.
martini_v2.0_lipids.itp |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Forcefield Parameters
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Featuring lysoPCs, DPC, palmitoic acid.
martini_v2.0_surfactants.itp |
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Last Updated on Saturday, 23 January 2010 15:14 |
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Forcefield Parameters
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Currently cholesterol and cholesteryl oleate only.
martini_v2.0_cholesterol.itp |
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Last Updated on Saturday, 23 January 2010 15:14 |
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Forcefield Parameters
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Various saturated and unsaturated alkanes, alcohols, triglycerides, and many small organic solvents.
martini_v2.0_solvents.itp |
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Last Updated on Saturday, 23 January 2010 15:15 |
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Forcefield Parameters
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Sodium, chloride, calcium and more.
martini_v2.0_ions.itp |
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Last Updated on Saturday, 23 January 2010 15:17 |
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Forcefield Parameters
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All twenty amino acids.
martini_v2.1_aminoacids.itp |
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Last Updated on Saturday, 23 January 2010 15:14 |
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Forcefield Parameters
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Common mono- and disaccharides, and amylose.
martini_v2.0_sugars.itp |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Forcefield Parameters
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Currently PEG and PEO, and a G5 PAMAM dendrimer
martini_v2.0_polymers.itp |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Forcefield Parameters
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Molecules not fitting in other categories.
Currently contains topologies for voltage-sensitive dyes
martini_v2.0_other.itp |
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Last Updated on Saturday, 23 January 2010 15:15 |
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Example Applications
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Equilibrated at T=300K, P=1 bar.
System size: water 2000 (corresponding to 8000 real water molecules).
water.growater.mdp
water.top
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Last Updated on Saturday, 23 January 2010 15:15 |
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Hexadecane slab in water. |
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Example Applications
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Equilibrated at T=300K, constant area and perpendicular Pz=1 bar.
System size: hexadecane 100, water 400.
hexadecane_slab.grohexadecane_slab.mdp
hexadecane_slab.top
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Last Updated on Saturday, 23 January 2010 15:15 |
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Example Applications
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Equilibrated at T=300K, P=1 bar.
System size: sodium 8, chloride 8, water 388.
nacl+wat.gronacl+wat.mdpnacl+wat.top
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Last Updated on Saturday, 23 January 2010 15:15 |
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Example Applications
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Equilibrated at T=325K, zero surface tension.
System size: lipids 128, water 2000.
dppc_bilayer.gro dppc_bilayer.mdp dppc_bilayer.top |
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Last Updated on Saturday, 23 January 2010 15:14 |
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Example Applications
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Equilibrated at T=300K, zero surface tension.
System size: lipids 128, water 1500.
dopc_bilayer.grodopc_bilayer.mdp
dopc_bilayer.toppope_bilayer.gropope_bilayer.mdppope_bilayer.top |
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Last Updated on Saturday, 23 January 2010 15:16 |
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Example Applications
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Equilibrated at T=300K, zero surface tension.
System composition: DPPC 38, cholesterol 16 (0.3 mole fraction), water 350.
dppc_chol.gro dppc_chol.mdp dppc_chol.top |
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Last Updated on Saturday, 23 January 2010 15:13 |
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Poly-unsaturated lipid/cholesterol bilayer |
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Example Applications
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Equilibrated at T=298K, zero surface tension.
System composition: DAPC 38, cholesterol 4 (0.1 mole fraction), water 142.
dapc_chol.grodapc_chol.mdpdapc_chol.top |
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Last Updated on Saturday, 23 January 2010 15:16 |
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Example Applications
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Equilibrated at T=295K, zero surface tension.
System composition: DPPC 828, Di-C18:2-PC 540, cholesterol 576 (0.42:0.28:0.3 ratio), water 12600.
raft.gro
raft.mpd
raft.top |
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Last Updated on Saturday, 23 January 2010 15:15 |
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Solvated DOPC and POPE vesicles |
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Example Applications
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Equilibrated at T=325K, P=1 bar.
System size: lipids 877, water 61552
(the DPPC vesicle is in a cubix box, the DOPE vesicle in an octahedral box)
dppc_vesicle.gro dppc_vesicle.mdp dppc_vesicle.top pope_vesicle.gro pope_vesicle.mdp pope_vesicle.top |
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Last Updated on Saturday, 23 January 2010 15:15 |
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Example Applications
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Non-equilibrated, expected to form an inverted hexagonal phase at T > 330K.
System composition: lipids 1024, water 800.
dope_2bilayer_lowhydration.grodope_2bilayer_lowhydration.mdpdope_2bilayer_lowhydration.top |
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Last Updated on Saturday, 23 January 2010 15:17 |
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Example Applications
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Equilibrated at T=300K, P=1 bar.
System composition: surfactants 54, water 6400.
dpc.grodpc.mdpdpc.top |
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Last Updated on Saturday, 23 January 2010 15:17 |
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Example Applications
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The toy peptide contains all amino acids.
Half of the peptide is helical, the other half beta strand.
Equilibrated at T=300K, P=1 bar.
System composition: 1 peptide, water 1538.
toypeptide.gro toypeptide.mdp toypeptide.top toypeptide.itp |
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Last Updated on Saturday, 23 January 2010 15:16 |
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Example Applications
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Equilibrated at T=300K, constant pressure P=1 bar.
System size: 56 peo polymers (of 36 monomers), water 13312.
peo36.gropeo36.mdp
peo36.top
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Last Updated on Saturday, 23 January 2010 15:17 |
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Example Applications
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Voltage sensitive dye Di-4-ASPBS bound to a POPC membrane
System size: 1 dye, lipids 128, water 1489.
dye1.grodye1.mdp
dye1.topdye1.ndx
A charged voltage sensitive dye Di-12P-ASPBS bound to a POPC membrane
System size: 1 dye, 2 sodium counterions, lipids 128, water 1481
dye4.grodye4.mdp
dye4.topdye4.ndx |
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Last Updated on Saturday, 23 January 2010 15:18 |
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