Downloads

Here you can find pointers to what the lab has to share; mostly software and models. Complementary Martini material is also available from the Martini website's download section.

Enjoy!

Analysis software

MDAnalysis

MDAnalysis is a powerful Python package to access topology and coordinate information from simulation data. Manuel is part of its developer team. Find more information in the project's page.

MDreader

Manuel wrote MDreader as an extension to MDAnalysis that seamlessly automates the paralellization of analysis scripts. Parallel invocation can be done either locally to a node or over several interconnected nodes using MPI. This allows scalability to match the resources typically available at HPC clusters.

Scripts/Models

Room for Improvement in the Initial Martini 3 Parameterization of Peptide Interactions

J. Karl Spinti, Fernando Neiva Nunes and Manuel N. Melo

Download here the models and analysis results from this work.

Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies

Filipe M. Sousa, Luís M. P. Lima, Clément Arnarez, Manuela M. Pereira, and Manuel N. Melo

J. Chem. Inf. Model. (2021). Manuscript DOI: 10.1021/acs.jcim.0c01077

Get updated parameterized models and other relevant files from the GitHub repo.

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

S. Dadsena, S. Bockelmann, J. G. M. Mina, D. G. Hassan, S. Korneev, G. Razzera, H. Jahn, P. Niekamp, D. Müller, M. Schneider, F. G. Tafesse, S. J. Marrink, M. N. Melo, J. C. M. Holthuis

Nature Communications (2019) 10. Manuscript DOI:10.1038/s41467-019-09654-4

Download here the models and analysis scripts used in this work.

A Martini 2 CG tocopherol model

If you use this model, please cite:

ACS Nano, 2018, 12 (10), pp 9855–9865
DOI: 10.1021/acsnano.8b01422