SARS-CoV-2 model



The group of Chen Song has published a fully-atomistic model of the SARS-CoV-2 envelope, including N-bound RNA segments, obtained after backmapping from a 500 ns Martini simulation (final configuration shown on the left).

For details, see:  Wang et al., Quant. Biology, 2023.

Martini condensates



Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation.

For details, check the paper from Ingolfsson et al. that just appeared in Biophysical Journal:

Self-assembling nanotubes


"Watching Molecular Nanotubes Self-Assemble in Real Time", JACS online Visualization by Marìck Manrho

Martini 3 LPS

New models for lipopolysaccharides are now available for Martini 3 ! See the paper from Vaiwala and Ayappa, Parameters can be found in the SI of their paper.

Membrane buckling artefact

In MD simulations using the GROMACS package with default Martini parameters, the group of Hummer found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, they identified overly short outer cutoffs and infrequent neighbor list updates that result in missed long-range attractive Lennard-Jones interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. Guidelines are presented to avoid these artefacts, including estimates for appropriate values for the outer cutoff r_l and the number of time steps nstlist between neighbor list updates.

Must-read for those who simulate membrane systems. For details, see the paper from Kim et al. in chemRxiv