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Follow \@tcbguiucMolecular simulations of biological systems span a variety of programs, each with its own file format. To bring them all into a single viewer, VMD 2 has now a new molfile reader, which opens the HDF5-based H5MD trajectories written by GROMACS 2026, HOOMD-blue GSD soft-matter simulations, and OpenMiChroM / Nucleome Data Bank CNDB chromatin models, plus cheminformatics SDF chemical tables and a modernized trajectory reader. It also includes a rewritten GROMACS reader, that loads structures about three times faster. A companion helper loads only a specified subset of the structure, making cell-scale systems even easier to visualize and analyze.
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.
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Computer Modeling in Bionanotechnology-The History
Since 2001 Illinois scientists have innovatively used molecular dynamics to simulate biological molecules combined with nanodevices. It turns out that the computational microscope is the quintessential imaging tool for these bionano systems. By Lisa Pollack.
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Recent Publications All Publications
- Probing Solution Dynamics of Tissue Factor Using Molecular Dynamics Simulations Guided by NMR Chemical Shifts. J. Phys. Chem. B, 2026.
- Elucidating the binding and metabolic interactions of sunitinib and sorafenib with cytochrome P450s CYP2U1 and CYP2D6. Mol. Pharmacol., 108(4):100114. 2026.
- LetA defines a structurally distinct transporter family. Nature, 651(8107): 1097–1106. 2026.
- Single-Molecule Electron Transport in Peptoids. J. Phys. Chem. B, 130(11):3054–3064. 2026.
- Cholesterol efflux protein, ABCA1, supports anticancer functions of myeloid immune cells. Sci. Adv., 12(1):eadx5490. 2026.
- Thermodynamic and Kinetic Analysis of Molecular Conformational Dynamics in a Riemannian Framework. J. Phys. Chem. A, 130(5):1220–1232. 2026.
- Simulating Gas Permeation Through the Central Pore of AQP5. Adv Exp Med Biol., 1498:105–113. 2026.
Highly Cited
NAMD - A parallel, object-oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996.
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