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Made with VMD

Biological membranes are complex assemblies of diverse lipids, and molecular dynamics (MD) simulation has been among the most effective biophysical tools to investigate them at an atomic-detailed level. Nevertheless, capturing the wide range of lipid compositions and their mixing continues to pose a major challenge to simulations, due to the very slow diffusion of lipids. This issue is particularly important when membrane proteins are present in the membrane and one is interested in studying how they interact with lipids. One solution to partially address this problem is to randomize the initial configuration of lipids in replicate simulations. The Center has developed a toolkit to rapidly clone a membrane with a specific lipid composition into as many copies (with shuffled lipids) as needed within a matter of minutes. The Membrane Mixer Plugin (MMP) uses advanced features in NAMD to remove clashes and make room before shuffling the lipids; it also performs several checks to test the quality of the generated membranes. This method can be accessed via a user-friendly GUI interface in the latest version of VMD.
Editorials

The Future of Biomolecular Modeling

A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more

Computational Biology of Membrane Proteins

Since 1988 Illinois researchers have consistently honed their skills in parallel computing, which enabled them to elucidate dynamic processes occurring in many membrane proteins and produce exciting discoveries. By Lisa Pollack Read more

Announcements

NAMD and VMD share in COVID-19 Gordon Bell Special PrizeUIUC establishes oneAPI academic Center of ExcellenceSARS-CoV2 Simulations on Microsoft AzureArgonne Honors Fellow for COVID-19 Research Effort


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