Highlights of our Work

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The latest NAMD 3.0 releases provide GPU-resident molecular dynamics simulation support for external forces, now including Colvars and Tcl Forces. This support allows users to take advantage of a great variety of additional forces in their GPU-accelerated simulations and free energy calculations. The Colvars (collective variables) module and Tcl Forces scripting both provide mechanisms to define external forces between groups of atoms, allowing control over specific structural features during a simulation to enable the study of complex biomolecular processes and interactions. These valuable capabilities are now available from within NAMD's fastest simulation mode.
BmrCD, a multidrug transporter, plays a critical role in drug efflux in bacteria closely related to Staphylococcus aureus. The transporter harvests the energy of ATP to pump drugs out of the cell, thus creating resistance against drugs such as antibiotics. The mechanism of this pumping effect strongly relies on interactions with the lipids in the membrane. To elucidate these underlying protein-lipid interactions, we used VMD to model partially resolved cryo-EM lipids in BmrCD structures solved by the Mchaourab lab at Vanderbilt and simulated their behavior in a bulk membrane using GPU-accelerated NAMD 3.0 at the Center. Simulations revealed that BmrCD engages in an extensive network of interactions with lipids in multiple conformations, elucidating the stabilization of the solved structure. For more details, see our recent publication in Nature Communications.

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