Published October 6, 2023
| Version v1
Dataset
Open
MD simulation of a model Gram-positive bilayer membrane (60% PG, 35% lysyl-PG, 5% CL)
Description
Composition:
Model bilayer composition aimed at replicating the behavior of the Staphylococcus aureus membrane (See also Mohanan et al. Chem Sci 2020, 11, 4669: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8159255/)
Per leaflet we have 48 POPG (16:0 / 18:1; -1 net charge), 28 DPPGK (16:0 / 16:0; +1 net charge), 4 TOCL1 (18:1,18:1 / 18:1,18:1; -1 net charge), giving 60% PG, 35% lysyl-PG, 5% CL. Bilayer is symmetric.
Technical details:
OpenMM 7.5.1
CHARMM36m force field
6,712 TIP3P waters
150 mM KCl (64 K+, 16 Cl-)
Temperature = 303.15 K
Trajectory output every 100 ps
Trajectory length = 500 ns ( = 5,000 frames)
(Standard CHARMM-GUI relaxation protocol)
Files
Files
(2.6 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:a0baf5b8d0d89aec7d416251c7ac8802
|
6.0 MB | Download |
|
md5:bda94f2c8196c17f9d3b41458dae616f
|
3.4 MB | Download |
|
md5:b481e3d4f3ef8532826e88adc85fa6cb
|
9.1 MB | Download |
|
md5:939c0f52212b0828451deba1c459eb9f
|
2.6 GB | Download |
|
md5:e100ee75ecd0b69126597323c3cfb368
|
21.3 MB | Download |
|
md5:2881e60f7d1d057a3c62374cd8c76683
|
7.0 MB | Download |
|
md5:1535b480df3379aad7b3e4c836f7e61d
|
1.6 kB | Download |
|
md5:565091b87ab3fac07a5bf7d8b435a017
|
64 Bytes | Download |
|
md5:aee978148a02afaa67cb91d5c79d36cc
|
2.1 kB | Download |