Peptidoglycan model

A Martini model of bacterial cell wall peptidoglycan is now available, thanks to the nice work of Vaiwala et al. The parameters and other files can be found here.

Death is just the beginning ....

Check out a nice paper from Lucendo et al, in PNAS, showing how TM helix dimerization plays a role in apoptosis. Featuring the Martini 3 beta release, corroborated by atomistic simulations and experimental data.


Working with large systems containing multiple bilayers or other dynamic macroscopic objects? Check out the new MDVoxelSegmentation tool.

Bottom up versus top down

Cool paper on the phase behavior of liquid crystals, demonstrating the transferability of Martini, outperforming bottom up models:

T.D. Potter, M. Walker, M.R. Wilson. Self-assembly and mesophase formation in a non-ionic chromonic liquid crystal: insights from bottom-up and top-down coarse-grained simulation models. Soft Matter, 2020. online.

Cholesterol artefacts

Be aware of using proper mdp settings when simulating cholesterol, as it might cause artificial phase separation if you don't, according to Javanainen et al: arXiv:2009.07767