Other systems

Phytochemicals

Phytochemicals Initial structures for the five phytochemicals: capsaicin (cap), curucmin (cur), epigallocatechin gallate (EGCG), genistein (gen), and resveratrol (res); and those five phytochemicals in a POPC bilayer (512 POPC lipids, 6000 CG waters, and 48 phytochemicals each) simulated for 2 μs.

cap-CG.gro
cur-CG.gro
EGCG-CG.gro
gen-CG.gro
res-CG.gro
POPC-cap-2us.gro
POPC-cur-2us.gro
POPC-EGCG-2us.gro
POPC-gen-2us.gro
POPC-res-2us.gro

And the phytochemicals parameter file:

martini_v2.0_phytochemicals.itp

Docosane physisorption on graphite from heptane

System for simulation of preferred physisorption of long-chain alkane (6 beads, representing docosane) from short-chain alkane (2-bead, representing heptane).

REQUIRES special parameter files!

Starting conformation contains 18,000 graphite surface particles (5 layers) GRAP, and in total 600 docosane molecules (DOCO) and 16,200 heptane molecules (OCT).

DNA strand

Double stranded DNA, 12 base pair

(provided by Syma Khalid)

dna.vmd (to view the elastic network)

Voltage sensitive dyes

Voltage sensitive dye Di-4-ASPBS bound to a POPC membrane
System size: 1 dye, lipids 128, water 1489

dye1.gro
dye1.mdp
dye1.top
dye1.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.gro
dye4.mdp
dye4.top
dye4.ndx