LATEST NEWS
SARS-CoV-2 model
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- Last Updated: Friday, 08 December 2023 13:33
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
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- Last Updated: Saturday, 25 November 2023 20:20
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
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- Last Updated: Friday, 06 October 2023 15:42
"Watching Molecular Nanotubes Self-Assemble in Real Time", JACS online pubs.acs.org/doi/10.1021/ja Visualization by Marìck Manrho
Martini 3 LPS
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- Last Updated: Friday, 15 September 2023 13:08
New models for lipopolysaccharides are now available for Martini 3 ! See the paper from Vaiwala and Ayappa, https://doi.org/10.1021/acs.
Membrane buckling artefact
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- Last Updated: Tuesday, 25 July 2023 07:49
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