Atomistic simulations of DAPC/cholesterol bilayers with one cholesterol restrained to the membrane core

Membranes consisting of 260 DAPC and 28 (10 mol%) cholesterol molecules were simulated at various temperatures of 285, 298, 310, 320, and 333 K. Notably, one cholesterol molecule was restrained to the membrane core. The CHARMM36 force field [1] was used and the membranes were generated using CHARMM-GUI [2].

For simulations without a restrained cholesterol, see the other upload at DOI:

The simulations were run for 2 microseconds using the GROMACS simulation suite [3]. Simulation parameters are found in the common mdp file (note that the temperature varies between simulations).

The upload contains simulation inputs and outputs that allows the replication, extension, or analysis of the simulation data:

• Topology files (top) and molecular definitions (itp)
• Index files (ndx)
• A common run parameter file (mdp)
• A run input file (tpr)
• Trajectory file (xtc) written every 100 ps
• Energy file (edr)
• Log file (log)
• Final structure file (gro)
• Continue point file (cpt)

The files are named LLLL_AA_CHOLXX_CORE_TTT.FFF, where

• LLLL is the type of phospholipid
• AA stands for all atom (Coarse-grained data in a separate upload)
• CHOLXX stands for the cholesterol concentration (CHOL10 for 10 mol%)
• TTT is the temperature
• FFF is the tile type (see above)

Note that topologies/index files are the same regardless of temperature, and hence their file names do not have the TTT section.

[1] DOI: 10.1021/jp101759q

[2] DOI: 10.1021/acs.jctc.5b00935

[3] DOI: 10.1016/j.softx.2015.06.001