Trajectories of simulated lipid membranes interacting with antimicrobial peptidomimetic AMC-109 and simulation setup files

Trajectories of simulated lipid membranes with antimicrobial peptidomimetic AMC-109.
Trajectories are in GROMACS format ".xtc", the frame rate is 10 ns, and water and NaCl ions were omitted from the trajectory deposit to reduce the size to acceptable limits.

The molecules are described using MARTINI 3 coarse grained force field.
This repository contains a set of simulations with varying ratio of POPC:POPG lipids from
100% POPC, 0% POPG (denoted as "pg000p..") to
0% POPC, 100% POPG (denoted as "pg100p..").
Ratios between these two extremes go in steps of 10%,
e.g. "pg060p.." denotes 40% POPC, 60% POPG.

The  files with ".out" or ".xvg" suffix are properties analyzed from the simulation. Namely, they are:
- "thickness" : thickness of the membrane
- "apl" : area per lipid of the lipid membrane
- "numcont" : number of contacts between the peptidomimetic AMC-109 and the lipids
- "ordPars" : order parameters of the end tail segments of the sn-1 tail of POPC lipids.

More details about how these properties were generated can be found in the attached scripts (".sh" files) in this repository.

Sample topology files in GROMACS format (binary ".tpr" and ASCII ".itp") are provided to complete the description of the molecular topologies used to generate the presented simulations.

This repository was created as a Supporting Information to a scientific paper at Nature Communications,

Lateral membrane organization as target of an antimicrobial peptidomimetic compound, 2023.