Viewing lipid DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine)

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]

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]

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

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]