- 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:
- Last Updated: Friday, 06 October 2023 15:42
Martini 3 LPS
- 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
- 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
- Last Updated: Saturday, 17 June 2023 09:02
Chemical reactions with Martini ?? Indeed !!
See the paper by Selim Sami, explaining a pragmatic way to capture chemical reactivity in Martini with the clever use of virtual sites: https://doi.org/10.1021/acs.jctc.2c01186
All the required input files together with tutorials on its use are provided as SI.